Application of Immobilized Enzymes for Nanopore Library Construction

ABSTRACT

The present disclosure relates, according to some embodiments, to methods for preparing a library for sequencing. For example, a method may comprise (a) in a coupled reaction, (i) contacting a population of nucleic acid fragments with a tailing enzyme to produce tailed fragments, and (ii) ligating to the tailed fragments a sequencing adapter with a ligase to produce adapter-tagged fragments; and/or separating adapter-tagged fragments from the tailing enzyme and the ligase to produce separated adapter-tagged fragments and, optionally, separated tailing enzyme and/or separated ligase. In some embodiments, a tailing enzyme and/or a ligase used in library preparation may be immobilized enzymes.

SEQUENCE LISTING STATEMENT

This disclosure includes a Sequence Listing submitted electronically inascii format under the file name “NEB-424_ST25.txt”. This SequenceListing is incorporated herein in its entirety by this reference.

BACKGROUND

The nanopore sequencing platform provided by Oxford NanoporeTechnologies (ONT) is a third-generation sequencing approach to sequencelong DNA/RNA molecules through the change of electrical signals as theDNA/RNA passes through the nanopore on a membrane (Jaworski, E. and A.Routh, Parallel ClickSeq® and Nanopore sequencing elucidates the rapidevolution of defective-interfering RNAs in Flock House virus. PLoSpathogens, 2017. 13(5): p. e1006365; Weirather, J. L., et al.,Comprehensive comparison of Pacific Biosciences and Oxford NanoporeTechnologies and their applications to transcriptome analysis.F1000Research, 2017. 6; Wongsurawat, T., et al., Rapid sequencing ofmultiple RNA viruses in their native form. Frontiers in microbiology,2019. 10: p. 260; Zhao, L., et al., Analysis of transcriptome andepitranscriptome in plants using PacBio Iso-Seq® and nanopore-baseddirect RNA sequencing. Frontiers in Genetics, 2019. 10: p. 253).Nanopore direct RNA sequencing permits generation of full length,strand-specific RNA sequence reads. However, library prep practices withmultiple bead purification steps demand relatively high input of RNA orDNA, at least in part, because significant sample loss can occur duringthese steps. This bead purification procedure may also produce bias inbinding and elution of nucleic acid substrates of various lengths sothat the output doesn't precisely represent the input library. Inparticular, polynucleotides (e.g., long or ultralong RNA and DNAtemplates) may be subjected to breakage and precipitation during bead(e.g., AMPure® bead) purification.

SUMMARY

The present disclosure provides methods for preparing a library forsequencing. For example, a method may comprise (a) in a coupledreaction, (i) contacting a population of nucleic acid fragments with atailing enzyme to produce tailed fragments, and (ii) ligating to thetailed fragments a sequencing adapter with a ligase to produceadapter-tagged fragments; and/or separating adapter-tagged fragmentsfrom the tailing enzyme and the ligase to produce separatedadapter-tagged fragments and, optionally, separated tailing enzymeand/or separated ligase. In some embodiments, a tailing enzyme and/or aligase used in library preparation may be immobilized enzymes. Forexample, a tailing enzyme may be immobilized on a magnetic bead and/or aligase may be immobilized on a magnetic bead. Optionally, a tailingenzyme and a ligase may be immobilized on the separate supports orco-immobilized on a single support. A tailing enzyme and/or a ligase,according to some embodiments, may be soluble enzymes. In someembodiments, separating adapter tagged fragments may further comprisesubjecting the coupled reaction to a magnetic field (e.g., bringing thesample to a magnet, bringing a magnet to the sample, activating anelectromagnetic field). A population of nucleic acid fragments maycomprise ribonucleic acid fragments and/or may comprise deoxyribonucleicacid fragments. In some embodiments, methods may be capable of producingsequencing libraries with little input RNA. For example, methods may usea population of nucleic acid fragments having less than 100 ng ofnucleic acids or a population of nucleic acid fragments having less than10 ng of nucleic acids.

The present disclosure further provides methods for preparing sequencinglibraries comprise any combination of steps (a) and (b) and furthercomprise: (c) in a second coupled reaction, (i) contacting a secondpopulation of nucleic acid fragments with the separated tailing enzymeto produce additional tailed fragments, and (ii) ligating to theadditional tailed fragments a second sequencing adapter with theseparated ligase to produce additional adapter-tagged fragments, and/or(d) separating the additional adapter-tagged fragments from theseparated tailing enzyme and the separated ligase to produce separatedadditional adapter-tagged fragments, separated tailing enzyme, andseparated ligase. In some embodiments, a method comprise any combinationof steps (a), (b), (c), and (d) and may further comprise (e)translocating the separated adapter-tagged fragments through one or moretransmembrane pores; (f) detecting electrical changes as the one or moreseparated adapter-tagged fragments are translocated through the one ormore transmembrane pores in an insulating membrane to produce anelectrical signal; and/or (g) analyzing the electrical signal togenerate a sequence read. In some embodiments, one or more transmembranepores may retain about 90% of their initial activity after two hoursand/or may retain about 50% of their initial activity after 8 hours. Oneor more transmembrane pores, according to some embodiments of thedisclosure, may produce at least 900 sequence reads per transmembranepore. In some embodiments, a sequencing adapter may be a single-strandedadapter and may comprise a leader sequence; and a first sequence and asecond sequence, wherein the first and second sequences arecomplementary to each other and define a hairpin, wherein the leadersequence is configured to thread into the one or more transmembranepores.

BRIEF DESCRIPTION OF THE FIGURES

The file of this patent contains at least one drawing executed in color.Copies of this patent with color drawing(s) will be provided by thePatent and Trademark Office upon request and payment of the necessaryfee.

FIG. 1A-E schematically illustrates five methods for preparing nucleicacid libraries for sequencing (e.g., Nanopore MinION® sequencing). FIG.1A shows library construction in two sequential enzymatic steps usingsoluble enzymes without AMPure® bead purification (Sol without BP). FIG.1B shows library construction in two sequential enzymatic steps usingsoluble enzymes with AMPure® bead purification (Sol-seq). FIG. 1C showslibrary construction in a coupled enzymatic reaction using solubleenzymes with AMPure® bead purification (Sol-cpl). FIG. 1D shows libraryconstruction in two sequential enzymatic steps using immobilized enzymeswithout bead purification (Im-seq). FIG. 1E shows library constructionin a coupled enzymatic reaction using immobilized enzymes without beadpurification (Im-cpl).

FIG. 2 shows that poly(A) extension is dependent on poly(A) polymeraseconcentration. An RNA 45-mer oligo strand was treated with differentconcentrations of untagged poly(A) polymerase from NEB and poly(A)tailing activity of poly(A) polymerase was evaluated by capillaryelectrophoresis (CE).

FIG. 3 shows that poly(A) extension is dependent on the concentration ofpoly(A) polymerase-SNAP fusion protein. An RNA 45-mer oligo strand wastreated with different concentrations of a poly(A) polymerase-SNAPfusion protein and poly(A) tailing activity of was evaluated bycapillary electrophoresis (CE).

FIG. 4 shows poly(A) polymerase immobilization on PEG₇₅₀ coatedO⁶-benzylguainine (B G) beads.

FIG. 5 shows that poly(A) extension is dependent on the concentration ofan immobilized poly(A) polymerase. An RNA 45-mer oligo strand wastreated with different concentrations of an immobilized poly(A)polymerase and poly(A) tailing activity was evaluated by capillaryelectrophoresis (CE).

FIG. 6 shows that poly(A) tailing activity from soluble or immobilizedSNAP-tagged poly(A) polymerase (PAP). The following four reactionsamples (from top to bottom) were analyzed by CE technique: Sample 1,45-mer RNA oligo substrate without enzymatic treatment; Sample 2,substrate treated with soluble PAP; Sample 3, substrate reacted with PAPimmobilized to BG-magnetic beads without PEG₇₅₀-coated; sample 4:substrate reacted with PAP immobilized to PEG₇₅₀-coated BG magneticbeads. Sample 2 and Sample 4 displayed poly(A) tailing activity.

FIG. 7 shows relative activity of T4 DNA ligase immobilized on magneticbeads stored at −20° C. or 25° C. over a period of 7 days. The activityat day 1 is normalized to 100%.

FIG. 8 shows that T4 DNA ligase immobilized on agarose beads is morethermostable than two soluble T4 DNA ligases. Heat treatment wasconducted with two soluble T4 DNA Ligases, untagged T4 DNA Ligase (NEBM0202) and SNAP-tagged T4 DNA Ligase (HS-T4 DNA Ligase), and immobilizedT4 DNA Ligase (HS-T4 DNA Ligase-Agarose). Ligase activity was monitoredusing FMA-labeled synthetic double-stranded DNA (FAM-dsDNA). Thesubstrate/enzyme mixtures were treated at various temperatures (40°C.-100° C.), followed by incubation at 4° C. overnight. Fluorescent gelscanning was used to visualize substrate and ligation products(including the major product, termed Product), as detected in positivecontrols when the reactions were pre-treated at 4° C. but were absent inthe negative controls (NO Enzyme).

FIG. 9 shows that SNAP-tagged T4 DNA Ligase immobilized onto agarosebeads displayed ligase activity after heat treatment at 45° C. for 30min but the soluble form showed little or no ligase activity under thesame conditions. Aliquots of HS-T4 DNA Ligase conjugated to BG-Agarosebeads were incubated for 30 min at 4° C. (A), 37° C. (B) or 45° C. (C),followed by ligation reactions at room temperature (23° C.) for 2 hours.The samples (in the same order) were loaded onto three PAGE gels forelectrophoretic separation, followed by fluorescent gel scanning. 1, NoEnzyme; 2, Ligase (untagged T4 DNA Ligase, NEB M0202); 3, HS-Ligase(SNAP-tagged T4 DNA Ligase); 4, Ligase-Agarose; 5, Ligase-Chitin; 6,Ligase-Mag; 7, Ligase-SiM. Arrows indicate the expected positions ofligation product for soluble T4 DNA Ligase (arrows in lane 2) orLigase-Agarose (arrows in lane 4).

FIG. 10 shows that SNAP-tagged T4 DNA Ligase immobilized onto agarosebeads displayed more ligase activity after heat treatment at 55° C. or65° C. than the soluble form, which had little or no ligase activityunder the same conditions. DNA ligation was monitored using afluorophore (FAM)-labeled DNA substrate. The reactions were incubatedfor 10 min at 4° C., 55° C. or 65° C., followed by ligation reactions at23° C. for 2 hours (FIG. 10A) or at 4° C. overnight (FIG. 10B). Thesamples were electrophoresed on PAGE gels, followed by fluorescent gelscanning Ligase, untagged T4 DNA Ligase, NEB M0202; HS-Ligase,SNAP-tagged T4 DNA Ligase; Ligase-Agarose, HS-T4 DNA Ligase immobilizedto BG-Agarose Beads; Ligase-Mag, HS-T4 DNA Ligase conjugated toBG-Magnetic Beads. Arrows indicate the major ligation product from thereactions with Ligase-Agarose.

FIG. 11 shows that immobilized enzymes can be reused for consecutivereactions. Data from reactions #1, #10, and #20 of twenty consecutiveligation reactions catalyzed by a single preparation of immobilized T4DNA ligase. Performance over these twenty reactions matches the resultsobserved in a single reaction with soluble T4 DNA ligase.

FIG. 12 shows number of direct RNA sequencing reads from librariesprepared by two methods. In the first, labeled Sol-seq, the library wasprepared by two sequential steps of poly(A) tailing and adaptorligation. In the second, labeled Sol-cpl, the library was prepared bycarrying out poly(A) tailing and adaptor ligation simultaneously.

FIG. 13 shows the poly(A) tailing and adaptor ligation activity fromimmobilized poly(A) polymerase and immobilized T4 DNA Ligase. Foursamples were examined by CE (from top to bottom): Sample 1, untreatedFAM-labeled RNA substrate showing a distinct peak; sample 2, FAM-labeledRNA substrate treated by immobilized Poly(A) polymerase; Sample 3,Sample 2 treated with immobilized T4 DNA ligase and RTA-poly(dT)₁₅;Sample 4, Sample 2 treated with immobilized T4 DNA ligase andRTA-poly(dT)₁₀. A bell-shaped peak in Sample 2 represents addition of 3′poly(A) tails of various length to the RNA substrate (Sample 1).Ligation of an RTA adaptor to the poly(A) tailed products generatedhigher molecular mass products resulting in a shift of the bell-shapedpeak to the right.

FIG. 14 compares Nanopore RNA sequence reads obtained with librariesprepared by different methods. Each library was prepared using solubleenzymes without bead purification (Sol w/o BP), soluble enzymes withsequential poly(A) tailing and ligation with bead purification(Sol-seq), or immobilized enzymes with sequential poly(A) tailing andligation protocol without bead purification (Im-seq). 164 ng of RNAlibrary was used for each sequencing run.

FIG. 15 shows total sequence reads from Nanopore direct RNA sequencingof RNA libraries constructed with 500 ng input RNA using immobilizedenzymes without AMPure® bead purification following either sequentialreaction protocol (Im-seq) or coupled reaction protocol (Im-cpl). Afterenzymatic treatment enzyme-conjugated beads were pelleted on a magneticrack and the supernatants were transferred to a fresh tube. 105 ng oftotal RNA from each library was mixed with the solution provided by ONTbefore loading onto MinION® R9.1.4 flow cells for direct RNA sequencing.

FIG. 16A-B shows that co-immobilized enzymes displayed both poly(A)polymerase activity and T4 DNA ligase activity. FIG. 16A shows thatimmobilized poly(A) polymerase, co-immobilized with T4 DNA ligase, isactive in a poly(A) tailing assay in which a poly(A) tail is added to a35-mer RNA (lower panel), but not a corresponding control (upper panel).FIG. 16B shows that immobilized T4 DNA ligase, co-immobilized withpoly(A) polymerase on BG-modified beads (BGPL), displayed activity in anadapter ligation assay in which adapters RTA and RMX were ligated toeach other (lower panel), but not a control with RTA alone (upperpanel).

FIG. 17 shows an example of fully automated Nanopore sequencing workflowwhich includes library construction catalyzed by immobilized enzymes.

FIG. 18A-B shows the number of Nanopore RNA sequencing reads obtainedwith low-input RNA libraries prepared with immobilized enzymes. FIG. 18Ashows the number of sequencing reads obtained from 100 ng of Listeriamonocytogenes RNA libraries prepared using immobilized enzymes followingeither a sequential reaction method (“Im-seq 100”; Example 4D) or acoupled reaction method (“Im-cpl 100”; Example 4E) without AMPure® beadpurification. FIG. 18B shows the number of sequencing reads obtainedfrom 100 ng of mammalian RNA libraries prepared using immobilized ligase(“ImL”) or immobilized polymerase and immobilized ligase (“ImP & ImL”)without AMPure® bead purification. Each output library was loaded ontoNanopore R9.4.1. flow cells for direct RNA sequencing.

FIG. 19 shows a comparison of the number of Nanopore RNA sequencingreads obtained with RNA libraries prepared according to one of fivemethods: Sol-seq libraries were prepared with soluble enzymes and beadpurification using a sequential reaction protocol; Sol-cpl librarieswere prepared with soluble enzymes and bead purification using a coupledreaction protocol; Sol w/o BP libraries prepared with soluble enzymessequentially without bead purification; Im-seq libraries were preparedwith immobilized enzymes using the sequential reaction protocol withoutbead purification; Im-cpl libraries were prepared with immobilizedenzymes using the coupled reaction protocol without bead purification.The sequencing reads shown were obtained after 2 hour run time.

FIG. 20 shows a comparison of functional nanopores over time duringdirect RNA sequencing runs in ONT flow cells. Duplicate libraries wereprepared using each of the five protocols illustrated in FIG. 1A-E andthe resulting sequencing reads were displayed in FIG. 19.

FIG. 21 shows the sequence reads per nanopore from libraries prepared bythe coupled reaction method (square dots between 900 and 1100 ofnormalized reads) in comparison with those from the libraries preparedby the sequential reaction method with immobilized enzymes (circulardots between 200 and 500 of normalized reads). The orange curve alignsthe reads/pore data points from three sequencing samples with 83 ng, 109ng or 136.5 ng loaded on a flow cell. The blue curve aligns thereads/pore data points from four sequencing samples with various amountof RNA (38 ng, 39 ng, 105 ng and 164.4 ng) per flow cell.

FIG. 22 shows proposed DNA library preparation workflow for ONTsequencing platform. The workflow is comprised of three reactions,poly(dA) tailing catalyzed by terminal deoxynucleotidyl transferase(TdT), ligation of a 3′ Poly(dT)-containing adaptor with motor protein(red dot), and gap-filling and nick sealing with DNA polymerase (Pol)and DNA Ligase. Relevant soluble or immobilized enzymes can be utilizedto catalyze each enzymatic treatment. Enzymes may be removed,inactivated or present in the final sequencing library.

FIG. 23 shows a two-step reaction of poly(dA) tailing of a syntheticdouble-stranded DNA substrate (possessing a FAM probe) catalyzed by TdTand subsequent ligation with a synthetic adaptor, RTA-poly(dT)possessing a ROX probe. A ligated product can be detected by CE analysisdue to the presence of both FAM and ROX probes (as shown in FIG. 18C).

FIG. 24A-C shows sequential poly(dA) and ligation reactions withimmobilized enzymes. FIG. 24A shows poly(dA) tailing of 5′FAM-labeledDNA substrate by TdT in two different substrate-to-dATP ratios (1:100and 1:200). Incorporation of dAMP at the 3′ termini of 5′FAM-labeled DNAstrand and the length or range of poly(dA) can be detected by CEanalysis. FIG. 24B shows detection of a FAM-labeled DNA substrateligated to ROX-labeled RTA-Poly(dT) using FAM-detecting channel by CEanalysis. Top: FAM-labeled DNA substrate; Middle: FAM-labeled DNAsubstrate treated with TdT shows multiple species corresponding tovarious poly(dA) length; Bottom: the Poly(dA)-tailed DNA mixture furthertreated with T4 DNA Ligase in the presence of RTA-Poly(dT) exhibits ashift to a pool of higher molecular mass species with various length ofpoly(dA) tails. FIG. 24C shows detection of a FAM-labeled DNA substrateligated to ROX-labeled RTA-Poly(dT) by CE analysis. Top: FAM-labeled DNAsubstrate without enzyme treatment; Middle: FAM-labeled DNA substratetreated with TdT shows multiple species corresponding to various lengthof poly(dA) tails; Bottom: detection of the ligation products using bothFAM- and ROX-detecting channels (depicted in blue and red,respectively). The Poly(dA)-tailed DNA mixture (as presented in themiddle graph) treated with T4 DNA Ligase in the presence of RTA-Poly(dT)exhibits a shift to a pool of higher molecular mass species with variouslength of poly(dA) tails, with overlapping signals from FAM and ROXprobes.

FIG. 25 shows CE analysis of sequential Poly(dA) tailing and adaptorligation reaction products catalyzed by soluble and immobilized T4 DNAligase. FAM-labeled DNA substrate ligated to ROX-labeled RTA-Poly(dT) byTdT in a substrate-to-dATP ratio of 1:100. Subsequently, the reactionmedium containing the poly(dA)-tailed DNA products (pool), was incubatedwith either soluble or immobilized T4 DNA ligase and RTA-poly(dT)adaptor possessing 3′ poly(dT) and ROX probe. DNA substrate: FAM-labeledDNA substrate without enzyme treatment; TdT: FAM-labeled DNA substratetreated with TdT showing multiple species corresponding to variouslength of poly(dA) tails; TdT+Ligase: Poly(dA) tailed DNA treated by T4DNA Ligase was examined with both FAM- and ROX-detecting channels(depicted in blue and red, respectively). TdT+IM-Ligase: TdT-treated DNAwas treated with immobilized T4 DNA Ligase and examined with both FAM-and ROX-detecting channels (depicted in blue and red, respectively).RTA-Poly(dT): adaptor without enzymatic treatment. Co-localization ofthe fluorescence signals of FAM (blue) and ROX (red) indicates ligationof the 5′ FAM-labeled DNA pool to the 3′ ROX-labeled strand of theadaptor.

FIG. 26 shows schematic diagrams of two methods of DNA libraryconstruction. FIG. 26A shows library construction using soluble enzymeswith an AMPure® bead purification step. FIG. 26B shows libraryconstruction using immobilized DNA modifying enzymes without AMPure®bead purification.

FIG. 27 shows end repair, dA-tailing and adaptor ligation of syntheticDNA modified using immobilized enzymes with products of each stepsubjected to CE analysis. This method is designed for construction ofNanopore DNA library without use of AMPure® bead purification andPEG-based buffer.

DETAILED DESCRIPTION

The present disclosure generally relates to methods and compositions forpreparing polynucleotide libraries. Polynucleotide libraries, in someembodiments, may be prepared for sequencing using the disclosed methodsand compositions. In some embodiments, compositions comprisingpolynucleotides (e.g., fragments) may be subjected to coupled reactionsin which soluble enzymes, immobilized enzymes, or both soluble andimmobilized enzymes repair or condition the ends of the polynucleotides,tail one or both ends, and/or ligate the polynucleotides to a sequencingadapter. One or more of the enzymes used may be immobilized on a bead(e.g., a magnetic bead) or other solid support. For example, in acoupled reaction comprising a tailing reaction and a ligation reaction,a tailing enzyme and a ligase may be immobilized on separate supports orco-immobilized on a common support Immobilized enzymes may reduce orobviate the need for damaging bead purification steps. Bead purificationmay be used to remove soluble enzymes and other compounds in thereaction media, but may also damage the polynucleotides being purifiedand may introduce contaminating chemicals present on the beads or inrequired wash solutions (e.g., ethanol and PEG among others) that mayinterfere with subsequent uses of the purified polynucleotides (e.g.,sequencing). Library preparation methods using immobilized enzymes mayrequire lower amounts of input polynucleotides to achieve the samenumber of sequencing reads and may better preserve the activity oftransmembrane pores used in sequencing. Library preparation andsequencing workflows using immobilized enzymes may be automated and mayinclude reuse of immobilized enzymes, preserving reagents and loweringcosts.

Aspects of the present disclosure can be further understood in light ofthe embodiments, section headings, figures, descriptions and examples,none of which should be construed as limiting the entire scope of thepresent disclosure in any way. Accordingly, the claims set forth belowshould be construed in view of the full breadth and spirit of thedisclosure.

Each of the individual embodiments described and illustrated herein hasdiscrete components and features which can be readily separated from orcombined with the features of any of the other several embodimentswithout departing from the scope or spirit of the present teachings. Anyrecited method can be carried out in the order of events recited or inany other order which is logically possible.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure belongs. Still, certain terms aredefined herein with respect to embodiments of the disclosure and for thesake of clarity and ease of reference.

Sources of commonly understood terms and symbols may include: standardtreatises and texts such as Kornberg and Baker, DNA Replication, SecondEdition (W.H. Freeman, New York, 1992); Lehninger, Biochemistry, SecondEdition (Worth Publishers, New York, 1975); Strachan and Read, HumanMolecular Genetics, Second Edition (Wiley-Liss, New York, 1999);Eckstein, editor, Oligonucleotides and Analogs: A Practical Approach(Oxford University Press, New York, 1991); Gait, editor, OligonucleotideSynthesis: A Practical Approach (IRL Press, Oxford, 1984); Singleton, etal., Dictionary of Microbiology and Molecular biology, 2d ed., JohnWiley and Sons, New York (1994), and Hale & Markham, the Harper CollinsDictionary of Biology, Harper Perennial, N.Y. (1991) and the like.

As used herein and in the appended claims, the singular forms “a” and“an” include plural referents unless the context clearly dictatesotherwise. For example, the term “a protein” refers to one or moreproteins, i.e., a single protein and multiple proteins. It is furthernoted that the claims can be drafted to exclude any optional element. Assuch, this statement is intended to serve as antecedent basis for use ofsuch exclusive terminology as “solely,” “only” and the like inconnection with the recitation of claim elements or use of a “negative”limitation.

Numeric ranges are inclusive of the numbers defining the range. Allnumbers should be understood to encompass the midpoint of the integerabove and below the integer i.e., the number 2 encompasses 1.5-2.5. Thenumber 2.5 encompasses 2.45-2.55 etc. When sample numerical values areprovided, each alone may represent an intermediate value in a range ofvalues and together may represent the extremes of a range unlessspecified.

In the context of the present disclosure, “adapter” refers to a sequencethat is joined to or can be joined to another molecule (e.g., ligated orcopied onto via primer extension). An adapter can be DNA or RNA, or amixture of the two. An adapter may be 15 to 100 bases, e.g., 50 to 70bases, although adapters outside of this range are envisioned. In alibrary of polynucleotide molecules that contain an adapter (e.g., a 3′or 5′ adapter, the adapter sequence used is not present in the DNAsequences under examination (i.e., the sequence in between theadapters). For example, if the library of polynucleotide moleculescontains sequences derived from mammalian genomic DNA, cDNA or RNA, thenthe sequences of the adapters are not present in the mammalian genomeunder study. In many cases, the 5′ and 3′ adapters are of a differentsequence and are not complementary. In many cases, an adapter will notcontain a contiguous sequence of at least 8, 10 or 12 nucleotides thatis found in the DNA under examination. Adapters may be designed to servea specific purpose. For example, adapters may be designed for use insequencing applications. Sequencing adapters may comprise, for example,an oligo-(dT) overhang, a barcode sequence, an overhang (other thanoligo-(dT)) to anneal to another adapter, a site for anchoring a motorprotein, and a sequence to bind to tethering oligos with affinity topolymer membrane for guiding a DNA or RNA fragment (on which it resides)to the vicinity of a nanopore, and combinations thereof.

In the context of the present disclosure, “adapter-containing” refers toeither a nucleic acid that has been ligated to an adapter, or to anucleic acid to which an adapter has been added by primer extension. Insome embodiments, the adapters of a library of nucleic acid moleculesmay be made by ligating oligonucleotides to the 5′ and 3′ ends of themolecules (or specific sequences of the same) in an initial nucleic acidsample, e.g., DNA or genomic DNA, cDNA.

In the context of the present disclosure, “bead purification” refers touse of magnetic beads to preferentially adsorb polynucleotide molecules(e.g., RNA, DNA) away from soluble enzymes (and optionally, othercomponents) through a series of binding, washing, and elution steps.

In the context of the present disclosure, “coupled reaction” refers to areaction in which two or more reaction steps occur in a single reactionmixture and in a single reaction vessel (e.g., a tube, a well, acapillary, a flow cell, a surface). Sequential reaction steps in acoupled reaction may begin and/or continue without changes to reactionconditions (e.g., without addition or removal of reagents, changes intemperature, pH, volume, or washing) beyond those that arise or followfrom the reactions themselves. For example, a coupled reaction mayinclude a reaction in which a polymerase (e.g., an immobilizedpolymerase) is combined in a single reaction vessel with a ligase (e.g.,an immobilized ligase) and both tailing and ligation reactions proceedin the same mixture (e.g., without an intervening bead purification).For clarity, coupled reactions include reactions in whichmicroenvironments may exist (e.g., on the surface of individualmicrobeads in the reaction mixture).

In the context of the present disclosure, “fragment” refers to apolynucleotide. A fragment may originate from in vitro or in vivosynthetic processes. A population of fragments may include full-lengthpolynucleotides (as originally synthesized) and/or smaller portions ofsuch full-length sequences resulting from mechanical, chemical, and/orenzymatic breakage.

In the context of the present disclosure, “immobilized” refers tocovalent attachment of an enzyme to a solid support with or without alinker. Examples of solid supports include beads (e.g., magnetic,agarose, polystyrene, polyacrylamide, chitin). Beads may include one ormore surface modifications (e.g., O⁶-benzyleguanine, polyethyleneglycol) that facilitate covalent attachment and/or activity of an enzymeof interest. Non-covalent attachment (e.g., avidin:biotin, chitin:CBP)may also be useful in some embodiments, for example, where the level ofdissociation of the binding partner is deemed tolerable.

In the context of the present disclosure, “library” or “polynucleotidelibrary” refers to a mixture of different molecules. A library maycomprise DNA and/or RNA (e.g., genomic DNA, organelle DNA, cDNA, mRNA,microRNA, long non-coding RNAs or other RNAs of interest) or fragmentsthereof from any desired source (e.g., human, non-human mammal, plant,microbe, virus, or synthetic). A library may have any desired number ofdifferent polynucleotides. For example, a library may have more than10⁴, 10⁵, 10⁶ or 10⁷ different nucleic acid molecules. A library mayhave fewer different molecules, for example, where the moleculescollectively have more than 10⁴, 10⁵, 10⁶ or 10⁷ or more nucleotides. Insome embodiments, a library of polynucleotide molecules may be anenriched library, in which case the library may have a complexity ofless than 10%, less than 5%, less than 1%, less than 0.5%, or less than0.1%, less than 0.01%, less than 0.001% or less than 0.0001% relative tothe unenriched sample (e.g., a sample made from total RNA or totalgenomic DNA from a eukaryotic cell sample. Molecules can be enriched bymethods such as described in US2014/0287468 or US 2015/0119261. Alibrary, in some embodiments, may include member polynucleotides thatare tagged with an adapter.

In the context of the present disclosure, “ligase” refers to enzymesthat join polynucleotide ends together. Ligases include ATP-dependentdouble-strand polynucleotide ligases, NAD+-dependent double-strand DNAor RNA ligases and single-strand polynucleotide ligases. Ligases mayinclude any of the ligases described in EC 6.5.1.1 (ATP-dependentligases), EC 6.5.1.2 (NAD+-dependent ligases), EC 6.5.1.3 (RNA ligases)(see ExPASy Bioinformatics Resource Portal having a URL ofenzyme.expasy.org which is a repository of information concerningnomenclature of enzymes based on the recommendations of the NomenclatureCommittee of the International Union of Biochemistry and MolecularBiology (IUBMB) describing each type of characterized enzyme for whichan EC (Enzyme Commission) number has been provided. Specific examples ofligases include bacterial ligases such as E. coli DNA ligase and Taq DNAligase, Ampligase® thermostable DNA ligase (Epicentre® TechnologiesCorp., part of Illumina®, Madison, Wis.) and phage ligases such as T3DNA ligase, T4 DNA ligase, T7 DNA ligase, 9° N DNA ligase, and mutantsthereof. In some embodiments, a ligase may be included in a fusionprotein with a SNAP-tag protein.

In the context of the present disclosure, “magnetically gathering”refers to application of a magnetic field to a subject surface orcontainer. A magnetic field may be applied by forming a magnetic fieldat or near a surface or container, or by bringing a surface or containerinto the effective range of an existing magnetic field, for example, bymoving the surface or container near the existing field and/or byreshaping a field. Magnetically gathering immobilized enzymes into agroup may include forming a pellet of immobilized enzyme. Such pelletmay be sufficiently well formed and stable to tolerate manipulation orremoval of a fluid, composition, or reaction mixture adjoining and/or incontact with the pellet.

In the context of the present disclosure, “non-naturally occurring”refers to a polynucleotide, polypeptide, carbohydrate, lipid, orcomposition that does not exist in nature. Such a polynucleotide,polypeptide, carbohydrate, lipid, or composition may differ fromnaturally occurring polynucleotides polypeptides, carbohydrates, lipids,or compositions in one or more respects. For example, a polymer (e.g., apolynucleotide, polypeptide, or carbohydrate) may differ in the kind andarrangement of the component building blocks (e.g., nucleotide sequence,amino acid sequence, or sugar molecules). A polymer may differ from anaturally occurring polymer with respect to the molecule(s) to which itis linked. For example, a “non-naturally occurring” protein may differfrom naturally occurring proteins in its secondary, tertiary, orquaternary structure, by having a chemical bond (e.g., a covalent bondincluding a peptide bond, a phosphate bond, a disulfide bond, an esterbond, and ether bond, and others) to a polypeptide (e.g., a fusionprotein), a lipid, a carbohydrate, or any other molecule. Similarly, a“non-naturally occurring” polynucleotide or nucleic acid may contain oneor more other modifications (e.g., an added label or other moiety) tothe 5′-end, the 3′ end, and/or between the 5′- and 3′-ends (e.g.,methylation) of the nucleic acid. A “non-naturally occurring”composition may differ from naturally occurring compositions in one ormore of the following respects: (a) having components that are notcombined in nature, (b) having components in concentrations not found innature, (c) omitting one or components otherwise found in naturallyoccurring compositions, (d) having a form not found in nature, e.g.,dried, freeze dried, crystalline, aqueous, and (e) having one or moreadditional components beyond those found in nature (e.g., bufferingagents, a detergent, a dye, a solvent or a preservative).

In the context of the present disclosure, “tailing enzyme” refers totemplate-independent enzymes (e.g., polymerases, transferases) that addone or more nucleotides or ribonucleotides to the 3′ end of apolynucleotide. Tailing enzymes may add one or more As, one or more Gs,one or more Ts, one or more Cs, or one or more Us. Tailing enzymes maybe selected for specific applications based on their preference foradding a particular nucleotide or ribonucleotide, for example, tocompliment the end of an adapter to which the tailed polynucleotide.Examples of tailing enzymes include poly(A) polymerases, poly(G)polymerases, poly(U) polymerases, and terminal deoxynucleotidyltransferase (TdT). In some embodiments, a tailing enzyme may be includedin a fusion protein with a SNAP-tag protein.

In the context of the present disclosure, “transmembrane pore” refers toprotein pores and solid state pores. A transmembrane pore may be ananopore. Transmembrane protein pores may be or comprise hemolysin,leucocidin, lysenin, a Mycobacterium smegmatis porin (e.g., MspA, MspB,MspC, MspD), CsgG, an outer membrane porin (e.g., OmpF, OmpG), outermembrane phospholipase A, Neisseria autotransporter lipoprotein (NalP),WZA, or variants thereof.

In the context of the present disclosure, “unique molecule identifier”(UMI) refers to a random unique sequence of at least 6 nucleotides (6N).Longer random unique sequences may be used, for example, 2-15nucleotides, 6-12 nucleotides, or 8-12 nucleotides. UMIs may havesufficient sequence diversity to distinguish the molecule of which theyare a part (e.g., an adapter or a tagged fragment) from other moleculesin a mixture.

All publications (including all co-published supplemental and supportinginformation), patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, or patent application wasspecifically and individually indicated to be incorporated by reference.

FIG. 1A-E illustrates some embodiments of methods and compositionsdisclosed herein. For example, a method may include sequentiallycontacting an RNA composition (e.g., comprising one or more species ofRNA molecules) and a soluble tailing enzyme (optionally in the presenceof a buffer) to produce a polyA tailed RNA composition, contacting thepolyA tailed RNA composition with an adapter and a soluble ligase toproduce ligated products, washing the ligated products, eluting theligated products, and sequencing the ligated products (FIG. 1A).

A coupled method may include contacting an RNA composition (e.g.,comprising one or more species of RNA molecules), a soluble tailingenzyme, an adapter, and a soluble ligase (optionally in the presence ofa buffer) to produce ligated products, washing the ligated products,eluting the ligated products, and sequencing the ligated products (FIG.1B).

A method, in some embodiments, may include sequentially contacting anRNA composition (e.g., comprising one or more species of RNA molecules)and a soluble tailing enzyme (optionally in the presence of a buffer) toproduce a polyA tailed RNA composition, contacting the polyA tailed RNAcomposition with an adapter and a soluble ligase to produce ligatedproducts, and directly (e.g., without washing or elution) sequencing theligated products (FIG. 1C).

In some embodiments, a method may include sequentially contacting an RNAcomposition (e.g., comprising one or more species of RNA molecules) andan immobilized tailing enzyme (optionally in the presence of a buffer)to produce a polyA tailed RNA composition, removing the immobilizedtailing enzyme (e.g., in the case of enzymes bound to magnetic beads,magnetically gathering the magnetic beads into a group and taking awaythe polyA tailed composition, for example, by pipetting away from thebeads), contacting the polyA tailed RNA composition with an adapter andan immobilized ligase to produce ligated products, removing theimmobilized ligase (e.g., in the case of enzymes bound to magneticbeads, magnetically gathering the magnetic beads into a group and takingaway the ligated products, for example, by pipetting away from thebeads), and directly (e.g., without further washing or elution)sequencing the ligated products (FIG. 1D).

A coupled method, in some embodiments, may include contacting an RNAcomposition (e.g., comprising one or more species of RNA molecules), animmobilized tailing enzyme, an adapter, and an immobilized ligase(optionally in the presence of a buffer) to produce ligated products,removing the immobilized tailing enzyme and the immobilized ligase(e.g., in the case of enzymes bound to magnetic beads, magneticallygathering the magnetic beads into a group and taking away the ligatedproducts, for example, by pipetting away from the beads), and directly(e.g., without further washing or elution) sequencing the ligatedproducts (FIG. 1E).

With respect to its corresponding soluble enzyme, an immobilized enzymeis physically constrained to a support which defines a microenvironmentfor the immobilized enzyme molecules and its substrates. Surfaceenvironments (e.g. charges, functional groups, morphology,hydrophilicity) of the support materials can effect the enzymatic rateand immobilized enzyme stability. Therefore, improving and optimizingthis microenvironment may enhance or maximize enzymatic activities uponimmobilization. One or more strategies to alter surface microenvironmentmay be used to improve activity of immobilized enzymes. A singleoptimization solution may not applicable to all the enzymes. In someembodiments, various blocking groups or bead coatings (ethanolamine andpolyethylene glycol-PEG of different lengths) can be utilized to modifyhydrophilicity of support surface. For example, polyethylene glycol(PEG) moieties can be used to modify the surface of BG-functionalizedmagnetic beads. This PEG coating strategy has been shown to be effectivein enhancing activity of several enzymes validated, including T4 DNApolymerase, Taq DNA polymerase and T4 DNA ligase) (Li et al. 2018).According to some embodiments, the distance between the immobilizedenzyme and the beads surface may play a key role in retaining orreducing enzymatic activity. By using the proper conjugation chemistry,polyethylene glycol (PEG) linkage groups with variable length can beapplied as a spacer in between a SNAP-reactive BG and the bead surface.Various benzylguanine (BG) moieties (with PEGylated or non-PEGylatedlinkers) may confer different spatial arrangement of conjugated enzymemolecules. In some embodiments, solid phase catalysis strategicallyconsiders the substrate properties and accessibility which can beaffected by surface properties and enzyme orientation. In addition,CLIP-reactive benzylcytosine (BC) moieties can be utilized to substitutefor BG moieties on solid support because BC moieties are considered tobe more hydrophilic than BG moieties. With this strategy, a targetenzyme is fused to CLIP-tag instead of SNAP-tag. According to someembodiments, a bio-orthogonal conjugation strategy can simultaneouslyco-immobilize two enzymes in a desired molar ratio onto beadsfunctionalized with SNAP-reactive BG and CLIP-reactive BC moieties.Selection of support materials and proper modifications may enhanceenzymatic activity and thermostability. The surface properties canmodulate refolding upon relaxation and denaturation of enzyme globularstructures thereby maintaining or regaining activity after storage andheat treatment.

In RNA sequencing reactions or other applications using nanopores, thenanopores may be clogged, inactivated, and/or otherwise compromised byproteins that may be present in the compositions contacted with thenanopores. Accordingly, methods, applications, protocols and workflowsincluding nanopores may comprise removing proteins (e.g., solubleproteins) by bead purification to alleviate such fouling. In someembodiments, the need for bead purification may be reduced or obviatedby optimizing enzymatic reactions, for example, by reducing the amountsof enzymes used (e.g., effectively decreasing the ratio of enzyme toproduct in a reaction). Reducing the amount of enzyme(s) may reducenanopore fouling thereby extending the functional time of nanopores inflow cells. While a reduction in the quantity of enzymes used may applyto all proteins or all enzymes in a reaction, since each protein andenzyme may interact with a given nanopore differently, reductions may bemade on a more selective basis, targeting those that are more prone tofouling. As explained in more detail in the Example section below, FIG.14 & FIG. 19 show that it is possible to generate sequence reads fromlibraries without bead purification, confirming that optimization ofreactions with soluble enzymes enhance library preparation and/orperformance.

In some embodiments, a wide range of enzymes may be immobilized withoutloss or without substantial loss of activity including, for example, TaqDNA polymerase, T4 DNA polymerase (T4 DNA pol), T4 polynucleotide kinase(T4 PNK), T4 DNA ligase, polyA polymerase, Klenow (Exo-), T4 BGT, 9° NDNA ligase, Taq DNA ligase, Bst DNA pol 2.0, phi29 DNA pol, Vvn(nuclease), Gka Reverse transcriptase, Tbr Reverse transcriptase, RNaseA (catalytic mutants), PolyA polymerase, Beta-galactosidase, PNGaseF,Endo H, Endo S, Sialidase, Human carbonyl reductase, Human Aldosereductase, Drosophila aldehyde-ketone reductase (AKR).

For example, the current ONT protocol uses 3 ul of T4 DNA Ligase (NEBM202M 2000 units/ul) or 6000 units for 500 ng input library. Use ofimmobilized enzymes and/or coupled reactions may reduce the amount ofsoluble T4 DNA Ligase by 90% (i.e. use of 600 units of ligase) becausethe immobilized enzyme protocols validated used only 180 units. For lowinput RNA library (<100 ng input), enzyme consumption can be furtherlowered.

Enzyme immobilization may provide opportunities to enhance performanceof enzymatic processes, for example, by allowing faster and moreefficient production of products, at least in part, by reducing oreliminating purification steps needed for corresponding soluble enzymeprocesses, by reducing reactant and/or product losses from washingsteps, and/or by allowing enzymes to be reused in subsequent reactioncycles Immobilization may imbue bound enzymes with additionalthermostability and/or thermoactivity. For example, immobilized enzymesmay tolerate higher temperatures (even if they are not catalyticallyactive at such higher temperatures), which could be useful forapplications in which enzymes are reused. In some embodiments, enzymeimmobilization may allow soluble enzyme processes to be automated (orautomated more efficiently) Immobilization may also allow processes tobe more effective and/or efficient by reducing enzyme carry over tosubsequent steps.

In some embodiments, methods including immobilized enzymes may omit orexclude heat treatments to inactivate enzymes, bead purification steps,and/or sequencing pore clogging. Heat stress can lead to theaccumulation of 8-oxoguanine, deaminated cytosine, and apurinic DNAsites (AP-sites) in a cell (Bruskov V. I., Malakhova L. V., Masalimov Z.K., Chernikov A. V.//Nucleic Acids Res. 2002. V. 30. P. 1354-1363. 19.Lindahl T., Nyberg B.//Biochemistry. 1974. V. 13. P. 3405-3410. 20.Warters R. L., Brizgys L. M.//J. Cell Physiol. 1987. V. 133. P. 144-150.Elimination of bead purification may result in more uniformly sizedfragments in a library to be sequenced. Bead purification may result inalteration of a library such as size distribution; For example, large orsmall species may be lost more than the species in the middle size rangedue to either less binding (leading to more loss) or tighter bindingresulting in lower elution efficiencies. This step may also introduceimpurities (present in loading and wash solutions) that may affectperformance or parameters of nanopores such as signals or functioningtime.

According to some embodiments, methods including immobilized enzymes maybe adapted to and performed in microfluidic, lab-on-a-chip formats withenzymes immobilized on surfaces. For example, systems for single-cellRNA sequencing that produce RNA of a single cell may be adapted tocontact such RNA with a tailing enzyme and a ligase (coupled orsequentially) on a surface or in a microfluidics device.

The present disclosure provides embodiments in which purification ofnucleic acids is facilitated by combining enzymatic steps into a singlereaction and/or immobilizing enzymes on magnetic beads or othersupports. The present disclosure further provides embodiments in whichenzyme activity and/or thermostability is enhanced by immobilization onmagnetic beads or other supports.

In some embodiments, a method of preparing a library (e.g., a DNAlibrary, an RNA library) for sequencing (e.g., ONT sequencing) mayinclude in a coupled reaction, (a) contacting a population of nucleicacid fragments with a tailing enzyme to produce tailed fragments, and/or(b) ligating to the tailed fragments a sequencing adapter with a ligaseto produce adapter-tagged fragments. A method may further includeseparating adapter-tagged fragments from the tailing enzyme and theligase to produce separated adapter-tagged fragments and optionallyseparated tailing enzyme and/or separated ligase. A tailing enzyme, insome embodiments, may be or comprise immobilized tailing enzyme. Aligase, in some embodiments, may be or comprise immobilized ligase. Forexample, a tailing enzyme may be immobilized on a bead (e.g., a magneticbead) and/or a ligase may be immobilized on a bead (e.g., a magneticbead). Each immobilized enzyme may be attached to a separate support ormay be combined on a common support. Optionally, a tailing enzyme and aligase each may be immobilized on their own separate support or both maybe co-immobilized on a single support. In some embodiments, one or moreenzymes (e.g., a tailing enzyme and/or a ligase) may be soluble enzymes.For example, a method may include contacting one or more soluble enzymeswith one or more substrates in a liquid (e.g., aqueous) media. In someembodiments, a method may include contacting two enzymes (e.g., atailing enzyme and a ligase) with at least one substrate for at leastone of the two enzymes (e.g., DNA or RNA) in a coupled reaction. In someembodiments of a coupled reaction, at least one product of one of theenzymes is a substrate of the other enzyme. It may be desirable toselect reaction conditions to favor production of the product(s) thatare substrates of the other enzyme and minimize or avoid production ofanything that reduces the efficiency of any of the coupled reactionenzymes, but conditions may be adjusted to tolerate the presence of someunwanted products.

In some embodiments, separating adapter tagged fragments (e.g., whereone or more enzymes used are immobilized on magnetic beads) may furthercomprise subjecting the coupled reaction to a magnetic field. Subjectinga coupled reaction to a magnetic field may include accomplished in anymanner desired. For example, a coupled reaction may be moved into anexisting magnetic field, an existing magnet may be moved into effectiverange of a coupled reaction, or a magnetic field may be applied, forexample, by switching on an electromagnet within an effective distanceof a coupled reaction. In some embodiments, subjecting a coupledreaction to a magnetic field gathers magnetic beads in the coupledreaction forming a liquid fraction comprising, for example, reactionproducts, buffers, and solvent, but few, if any, magnetic beads) and abead fraction comprising, for example, magnetic beads, enzymes, andsolvent, but few, if any, reaction products. Gathered magnetic beads mayform a pellet or other aggregate that facilitates separation (e.g.,removal) of other reaction components (e.g., components remaining insolution).

A population of nucleic acid fragments may comprise ribonucleic acidfragments and/or may comprise deoxyribonucleic acid fragments. Fragmentsmay be of any desired size. For example, a population of nucleic acidfragments may comprise fragments ranging in length from 100 to 1000 nts,200 to 2000 nts, 500 to 5000 nts, 1,000 to 10,000 nts, 2,000 to 20,000nts, 5,000 to 50,000 nts, 10,000 to 100,000 nts, or combinationsthereof. A population of nucleic acid fragments may comprise fragmentsfrom any desirable source including, for example, fragments synthesizedor assembled in vitro and/or fragments of polynucleotides from microbes(e.g., yeast, bacteria, viruses, phage), fungi, plants, amphibians,reptiles, fish, mammals, birds, or any other organism.

In some embodiments, methods may be capable of producing sequencinglibraries with little input RNA. For example, methods may use apopulation of nucleic acid fragments having less than 100 ng of nucleicacids or a population of nucleic acid fragments having less than 10 ngof nucleic acids. In some embodiments, methods including coupledreactions and/or immobilized enzymes may produce more sequencing readsper mass of input DNA or RNA when compared with corresponding methodsthat do not include coupled reactions and/or immobilized enzymes. Forexample, methods including a coupled reaction and/or an immobilizedenzyme may produce 2×, 3×, 4×, 5×, 6×, 7×, 8×, 9×, 10×, 11×, 12× or moresequencing reads compared to methods including only sequential reactionswith soluble enzymes and bead purification.

The present disclosure further provides methods for preparing sequencinglibraries comprise any combination of tailing and/or ligating steps andfurther comprising reusing the tailing enzyme and/or the ligase. Forexample, a method may include, in a second reaction (e.g., a secondcoupled reaction), contacting a second population of nucleic acidfragments with the separated tailing enzyme (produced from the firstreaction) to produce additional tailed fragments, and ligating(optionally, with a ligase also recycled from the first reaction) to theadditional tailed fragments a second sequencing adapter with theseparated ligase to produce additional adapter-tagged fragments. Theadditional adapter-tagged fragments may be separated from the separatedtailing enzyme and the separated ligase to produce separated additionaladapter-tagged fragments, separated tailing enzyme, and/or separatedligase. In some embodiments, a method contacting separatedadapter-tagged fragments with one or more transmembrane pores (e.g., ONTnanopores) for sequencing. For example, a method may comprisetranslocating separated adapter-tagged fragments through one or moretransmembrane pores, (f) detecting electrical changes as the one or moreseparated adapter-tagged fragments are translocated through the one ormore transmembrane pores in an insulating membrane to produce anelectrical signal; and/or analyzing the electrical signal to generate asequence read. In some embodiments, one or more transmembrane pores(e.g., in contact with a population of adapter-tagged fragments) mayretain about 90% of their initial activity (e.g., translocationactivity) after two hours and/or may retain about 50% of their initialactivity after 8 hours. One or more transmembrane pores, according tosome embodiments of the disclosure, may produce at least 900 sequencereads per transmembrane pore. For example, the number of sequencingreads of a population of nanopores (e.g., in contact with a populationof adapter-tagged fragments) may be, on average, at least 900. In someembodiments, a sequencing adapter may be a single-stranded adapter andmay comprise a leader sequence; and a first sequence and a secondsequence, wherein the first and second sequences are complementary toeach other and define a hairpin, wherein the leader sequence isconfigured to thread into the one or more transmembrane pores.

Kits

The present disclosure further relates to kits including immobilizedenzymes. For example, a kit may include an immobilized tailing enzyme,an immobilized ligase, a polynucleotide (e.g., a population ofpolynucleotides) dNTPs, rNTPs, primers, buffering agents, and/orcombinations thereof. Immobilized enzymes may be included in a storagebuffer (e.g., comprising glycerol and a buffering agent). A kit mayinclude a reaction buffer which may be in concentrated form, and thebuffer may contain additives (e.g. glycerol), salt (e.g. KCl), reducingagent, EDTA or detergents, among others. A kit comprising dNTPs mayinclude one, two, three of all four of dATP, dTTP, dGTP and dCTP. A kitcomprising rNTPs may include one, two, three of all four of rATP, rUTP,rGTP and rCTP. A kit may further comprise one or more modifiednucleotides. A kit may optionally comprise one or more primers (randomprimers, bump primers, exonuclease-resistant primers,chemically-modified primers, custom sequence primers, or combinationsthereof). One or more components of a kit may be included in onecontainer for a single step reaction, or one or more components may becontained in one container, but separated from other components forsequential use or parallel use. The contents of a kit may be formulatedfor use in a desired method or process.

A kit is provided that contains: (i) an immobilized tailing enzyme; and(ii) a buffer or (i) an immobilized tailing enzyme; (ii) an immobilizedligase, and (iii) a buffer. An immobilized enzyme may have a lyophilizedform or may be included in a buffer (e.g., an aqueous buffer, a storagebuffer or a reaction buffer in concentrated form). A kit may contain theimmobilized enzyme in a mastermix suitable for receiving and amplifyinga template nucleic acid. An immobilized enzyme may be a purified enzymeso as to contain substantially no DNA or RNA and/or no nucleases. Areaction buffer for and/or storage buffers containing an immobilizedenzyme may include non-ionic, ionic e.g. anionic or zwitterionicsurfactants and crowding agents. A kit may include an immobilized enzymeand a reaction buffer in a single tube or in different tubes.

A subject kit may further include instructions for using the componentsof the kit to practice a desired method. The instructions may berecorded on a suitable recording medium. For example, instructions maybe printed on a substrate, such as paper or plastic, etc. As such, theinstructions may be present in the kits as a package insert, in thelabeling of the container of the kit or components thereof (i.e.,associated with the packaging or sub-packaging) etc. Instructions may bepresent as an electronic storage data file residing on a suitablecomputer readable storage medium (e.g. a CD-ROM, a flash drive).Instructions may be provided remotely using, for example, cloud orinternet resources with a link or other access instructions provided inor with a kit.

EXAMPLES

Some embodiments may be illustrated by one or more of the examplesprovided herein.

Example 1: Immobilization of Poly(A) Polymerase and Kinetics StudyExample 1A. Soluble Poly(A) Polymerase Alone

Poly(A) polymerase catalyzes poly(A) tailing at the 3′ end of RNA andthe resulting tails can be hybridized with and ligated to adapters(e.g., Nanopore Adaptors) for direct RNA sequencing. The kinetics ofpoly(A) polymerase (NEB M0276) at different concentrations was studiedas described in this Example 1. Reaction components (6 μL nuclease-freewater, 1 μL, 10× poly(A) polymerase reaction buffer (NEB), 1 μL 10 mMATP, 0.5 μL RNase inhibitor, 1 μL 1 μM RNA 45-mer oligo and 0.5 μLpoly(A) polymerase (at 12 nM, 24 nM, 60 nM or 120 nM)) were mixed andincubated at 37° C. for 20 min to allow poly(A) tailing. Each reactionwas quenched by addition of 10 μL 50 mM EDTA with 0.7% Tween-20, dilutedto a final volume of 200 μL, and sent for capillary electrophoresis (CE)analysis.

Results shown in FIG. 2 demonstrate that RNA oligo strands were extendedby addition of poly(A) tails at the 3′ end of the RNA with the presenceof poly(A) polymerase. More extensive strand extension was observed withincreasing the concentration of poly(A) polymerase from 0.6 nM to 6 nMfinal concentration.

Example 1B. Poly(A) Polymerase-SNAP-Tag® Fusion

Cells expressing a poly(A) polymerase-SNAP-Tag® fusion were harvested bycentrifugation and lysed by sonication on ice. The resulting lysate wascentrifuged and the clarified crude extract produced was purified on anickel column. After loading, the column was washed and the fusionprotein was eluted and dialyzed overnight. The enzyme concentration wasdetermined using Bradford assay.

The activity of the expressed fusion protein was evaluated according toExample 1A. Results shown in FIG. 3 demonstrate RNA 45-mer oligo strandextension by the purified poly(A) polymerase-SNAP fusion protein.Comparing FIG. 2 and FIG. 3 demonstrates that RNA 45-mer oligo strandextension by the poly(A) polymerase-SNAP fusion protein aligned wellwith the soluble NEB poly(A) polymerase.

Example 1C. Poly(A) Polymerase Immobilization on O⁶-Benzylguainine (BG)Magnetic Beads

O⁶-benzylguainine (BG) functionalized magnetic beads coated with PEG₇₅₀(100 μL of a 25% (v/v) slurry) were washed five times with 250 μL buffer(1×PBS, #9808, Cell Signaling, 1 mM DTT, 300 mM NaCl) for 5 times.Poly(A) polymerase-SNAP fusion protein (25 μg) in 125 μL buffer (1×PBSwith 300 mM NaCl), was mixed with the pre-washed BG beads, and incubatedat 4° C. overnight to immobilize the fusion protein (FIG. 4). The enzymebead mixture was washed with the same buffer 8 times to remove unboundprotein. Diluent C buffer without BSA (NEB) was used to resuspend thebeads with immobilized fusion protein for storage at −20° C.

The activity of the immobilized poly(A) polymerase was evaluatedaccording to Example 1A. Results shown in FIG. 5 demonstrate RNA 45-meroligo strand extension by the immobilized poly(A) polymerase-SNAP fusionprotein.

Example 2: Immobilized Poly(A) Polymerase Displays Stability IncludingThermostability

This example shows how to improve microenvironment for immobilizedenzymes by increasing hydrophilicity of bead surface by PEG coating.Poly(A) polymerase was immobilized to two types of O⁶-benzylguainine(BG) functionalized magnetic beads coated with or without PEG₇₅₀generally as described in Li, S et al, “Enhancing Multistep DNAProcessing by Solid-Phase Enzyme Catalysis on Polyethylene Glycol CoatedBeads” Bioconjugate Chem. 2018, 29, 7, 2316-2324 An aliquot of 100 μL of25% (v/v) bead slurry was washed five times with 250 μL buffer (1×PBS,#9808, Cell Signaling, 1 mM DTT, 300 mM NaCl) for 5 times. Poly(A)polymerase-SNAP fusion protein (25 μg) was dissolved in 125 μL buffer(1×PBS with 300 mM NaCl), combined with the washed BG beads, andincubated at 4° C. overnight to immobilize the fusion protein on thebeads. The immobilized poly(A) polymerase-SNAP fusion protein beads werewashed with the same buffer 8 times to remove any unbound protein.Diluent C buffer (NEB) with no BSA was used to resuspend the beads withimmobilized fusion protein for storage at −80° C.

Poly(A) tailing reactions were performed using the soluble andimmobilized poly(A) polymerase according to the protocols described inExample 1. The data shown in FIG. 6 demonstrate that SNAP-tagged poly(A)polymerase immobilized to PEG₇₅₀-coated magnetic beads displayed poly(A)tailing activity on a 45-mer RNA oligo whereas the same fusion proteinimmobilized to magnetic beads without PEG₇₅₀ coating displayed little,if any, detectable poly(A) tailing.

Example 3: Immobilized T4 DNA Ligase Displays Stability IncludingThermostability Example 3A. T4 DNA Ligase Immobilization on MagneticBeads and Stability Assays

This example provides immobilization of SNAP-tagged T4 DNA Ligase toBG-magnetic Beads and validation of storage stability at −20° C. and 25°C.

HS-T4 DNA Ligase protein was immobilized to BG-Magnetic-Beads by mixing100 μg protein per 400 μl of 25% (V/V) bead slurry at 4° C. overnight in1×PBS buffer containing 1 mM DTT, followed by extensive wash (8×). Theresulting immobilized enzyme was termed BG-HS-T4 DNA Ligase and storedat −20° C. or 25° C. for 7 days. Activity testing was performedaccording to the Determination of the Unit Activity of T4 DNA Ligase byCapillary Electrophoresis (CE) activity assay (One unit is defined asthe amount of enzyme required to give 40% to 70% (55%±15%) ligation of0.12 μM of synthesized double-stranded DNA oligos with Hind III ends in20 minutes at 16° C.

Results are shown in FIG. 7. No detectable decrease in enzyme activitywas observed at −20° C. and an approximately 30% reduction in ligaseactivity at 25° C. during the storage period.

Example 3B. T4 DNA Ligase Immobilization on Agarose Beads

This example demonstrates that immobilization can improvethermostability of SNAP-tagged T4 DNA ligase conjugated to BG-Agarosebeads (HS-T4 DNA Ligase Agarose) compared to free SNAP-tagged T4 DNAligase (HS-T4 DNA Ligase) or untagged T4 DNA ligase (NEB M0202). HS-T4DNA Ligase protein was immobilized to SNAP-Capture Pull-Down Resin (ahighly crosslinked agarose, NEB S9144), termed BG-Agarose, by mixing 100μg protein per 100 μl of 50% bead slurry at 4° C. overnight in 1×PBSbuffer containing 1 mM DTT, followed by extensive wash. The resultingimmobilized enzyme was termed HS-T4 DNA Ligase Agarose. Each immobilizedenzyme master mixture was made by mixing 32 μL of HS-T4 DNA LigaseAgarose, 20 μL of 10×T4 DNA Ligase Reaction Buffer and 74.64 μL of H2O;Two types of soluble enzyme master mixtures were made by mixing 8 μL ofT4 DNA Ligase (NEB M0202) or HS-T4 DNA Ligase, 20 μL of 10×T4 DNA LigaseReaction Buffer and 98.64 μL of H2O.

Example 3C. Comparison of Ligase Activity of Soluble and ImmobilizedLigases

A FAM-labeled DNA duplex was formed by annealing synthetic oligomer,Gene32FAM-fw3′A, /56-FAMN/CA TGG TGA TTA CGA TTC TTG CCC AGT ATG TCA ATACAT CAG TAA AAA TA (SEQ ID NO:1) and Gene32-rv5′p, /5Phos/AT TTT TAC TGATGT ATT GAC ATA CTG GGC AAG AAT CGT AAT CAC CATG (SEQ ID NO:2). A DNAsubstrate mixture was prepared by mixing 60 μL of 10 μM 5TAM-labeled DNAduplex with 3′A and 160.08 μL of 15 μM TA-Adaptor possessing a 3′T,5′75Phos/GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT C/ideoxyu/A CAC TCT TTCCCT ACA CGA CGC TCT TCC GAT CT-3′ (SEQ ID NO:3).

For heat treatment, an aliquot of 15.83 μL from an enzyme master mixturewas incubated at 4, 40, 60, 80, 90, 95 or 100° C. for 10 min, followedby addition of 9.17 μL of the DNA substrate mixture. All the ligationreactions were carried out at 4° C. overnight in a shaker. The sampleswere analyzed by electrophoresis on a 12% Tris-Glycine PAGE(Novex/Invitrogen) in 1×TAE Buffer for 2.5 hours at 25 mA (current).Results are shown in FIG. 8. The DNA species possessing FAM probe signalwas detected by scanning the PAGE gel with an 488 nm excitationwavelength on Typhoon Imager (GE Healthcare). DNA ligation resulted information of new species of larger molecular mass, absent in the controlreactions without ligase (No Enzyme). Both untagged T4 DNA ligase andsoluble HS-T4 DNA Ligase showed no detectable ligase activity aftertreatment in the temperature range of 60-100° C., indicating thatsoluble form was subjected to irreversible denaturation. In contrast,HS-T4 DNA Ligase immobilized to BG-Agarose beads retained enzymaticactivity after treatment in the same range of elevated temperaturetested.

Example 3D. Effect of Heat Treatment on Various Soluble and ImmobilizedProducts of T4 DNA Ligases

Four types of beads, Agarose (SNAP-Capture Pull-Down Resin, NEB S9144),Chitin, Magnetic beads (Mag), SiMag beads (SiM) were modified to possessbenzylguanine ligand, a substrate of SNAP-tag. SNAP-tagged T4 DNA Ligase(HS-T4 DNA Ligase) protein was immobilized to each type ofbenzylguanine-functionalized beads. A typical immobilization reactionwas performed by mixing 100 μg protein with an Agarose bead slurry at 4°C. overnight, followed by extensive wash. The resulting immobilizedenzyme was termed Ligase-Agarose, Ligase-Chitin, Ligase-Mag andLigase-SiM, respectively. Ligation reactions were set up by mixing thefollowing components in a final volume of 20 μL containing 1×T4 DNALigase Reaction Buffer, 0.5 μM FAM-labeled DNA duplex, 3.75 μM adaptor,and 1 μL of immobilized HS-T4 DNA Ligase or HS-T4 DNA Ligase (HS-Ligase)or T4 DNA Ligase (Ligase, NEB M0202S). The reaction mixtures wereincubated for 30 min at 4° C. (A), 37° C. (B) or 45° C. (C).Subsequently, all the reaction mixtures were incubated for 2 hours at23° C. for DNA ligation to proceed. The samples were analyzed byelectrophoresis on a 12% Tris-Glycine PAGE (Novex/Invitrogen) in 1×TAEBuffer for 2.5 hours at 25 mA (current). The DNA species possessing FAMsignal was visualized by scanning the PAGE gel with an 488 nm excitationwavelength on Typhoon Imager (GE Healthcare). Results are shown in FIG.9. DNA ligation resulted in formation of a product of higher molecularmass, which is absent in the control reactions without ligase (NoEnzyme).

All ligase-containing reactions except for Ligase-SiM showed ligaseactivity after treatment at 4° C. (FIG. 9A) or 37° C. (FIG. 9B) for 30min. FIG. 9C shows that after heat treatment at 45° C. HS-T4 DNA Ligaseimmobilized to BG-Agarose beads retained higher enzymatic activitycompared to the other immobilized ligase products. Both untagged T4 DNAligase (Ligase) and soluble HS-T4 DNA Ligase (HS-Ligase), however,showed no or residual ligase activity after treatment at 45° C. for 30min, indicating that these soluble form ligases was subjected toirreversible denaturation.

Example 3E. Effect of Heat Treatment on Various Soluble and ImmobilizedProducts of T4 DNA Ligases

SNAP-tagged T4 DNA Ligase (HS-T4 DNA Ligase) protein was immobilized toBG-Agarose Beads (SNAP-Capture Pull-Down Resin, NEB 59144) andBG-Magnetic Beads (Mag, 1 μm) functionalized with benzylguanine ligand.The resulting immobilized enzyme was termed Ligase-Agarose andLigase-Mag, respectively. Ligation reactions were set up by mixing thefollowing components in a final volume of 20 μL containing 1×T4 DNALigase Reaction Buffer, 0.5 μM FAM-labeled DNA duplex, 3.75 μM adaptor,and 1 μL of immobilized HS-T4 DNA Ligase or HS-T4 DNA Ligase (HS-Ligase)or T4 DNA Ligase (Ligase, NEB M0202S). The reaction mixtures wereincubated for 10 min at 4° C., 55° C. (B) or 65° C. Subsequently, thereaction mixtures were incubated either at 23° C. for 2 hours (FIG. 10A)or at 4° C. overnight (FIG. 10B). The samples were electrophoresed on a12% Tris-Glycine PAGE (Novex/Invitrogen) in 1×TAE Buffer for 2 hours at25 mA/gel. The DNA species possessing FAM probe were visualized byscanning the PAGE gel with an 488 nm excitation wavelength on TyphoonImager (GE Healthcare). Results are shown in FIG. 10. All positivecontrol reactions (4° C.) displayed ligase activity. Untagged T4 DNAligase (Ligase) and soluble HS-T4 DNA Ligase (HS-Ligase) as well asHS-T4 DNA Ligase immobilized onto Magnetic Beads (Ligase-Mag) showed noor residual ligase activity after treatment at 55° C. or 65° C. Incontrast, HS-T4 DNA Ligase immobilized to BG-Agarose Beads exhibitedsimilar enzymatic activity for each series of ligation reactions whenpre-treated at 4° C., 55° C. or 65° C., indicating that immobilizationto BG-Agarose Beads improved heat resistance of T4 DNA Ligase.

Example 3F. Reusing T4 DNA Ligase to Incorporate Unique MolecularIdentifiers (UMIs)

For next-generation sequencing, barcoding is an effective and commonlyused approach in multiplexed deep sequencing experiments. During thedemultiplexing step, identification of UMIs (barcodes) enables callingand quantification of the individual libraries which are pooled for asingle sequencing run. Furthermore, UMIs are increasingly used to tracknucleic acids from individual cells and to quantitatively assess theirclonal contributions over time. This example provides a workflow forefficiently producing libraries with UMIs that reuses immobilizedenzymes.

A typical library preparation protocol may consist of (a) repairing theends of the members of a population of nucleic acids, (b) A/dA-tailingrepaired members of the population, (c) ligating adapters to A/dA tailedmembers of the population, and (d) bead purification of adapter-taggedmembers of the population. Using immobilized enzymes in accordance withthis example obviates the need for bead purification and allows enzymesto be reused in subsequent cycles of library preparation.

In each cycle, a nucleic acid library may be ligated to an adapter witha bar code using immobilized enzymes in accordance with Example 4E toproduce an adapter tagged library. Immobilized enzyme beads (IM-Poly(A)polymerase and IM-ligase) are extensively washed, for example, at least5 times to remove residual barcoded adaptor, as demonstrated in theexperiment below and retained for reuse in the next cycle. A wash stepcan be incorporated to wash away residual bar-coded adaptor in eachcycle before an adaptor possessing a different barcode is ligated to RNAspecies from a fresh RNA sample. The number of cycles may be varied, andall resulting adapter-tagged libraries may be pooled for multiplexsequencing.

In this example, a preparation of 300 units of T4 DNA ligase immobilizedonto magnetic beads was utilized to perform repeated ligation of twoadaptors used for library construction for Nanopore direct RNAsequencing. One of the adaptor sequences was labeled with a 5′ FAM probeto detect and quantify the ligation product using capillaryelectrophoresis. In each reaction cycle, (a) an RNA library and theadapters were added to a vial containing the immobilized ligase andincubated at 25° C. for 10 min; (b) the enzyme-bearing beads werepelleted on magnetic rack; (c) the product-containing supernatant wasremoved from the vial and transferred for CE analysis; and (d) thepelleted beads were washed 5 times in conjunction withmicro-centrifugation in preparation for the next adaptor ligation cycle.

Results are shown in FIG. 11 and demonstrate efficient ligation in 20consecutive ligation reactions, which is indicative of reliability andreproducibility of immobilized T4 DNA ligase. In the control, soluble T4DNA ligase was used to carry out a single ligation reaction for the sameadaptor substrates.

Example 4: Library Preparation Using Soluble and Immobilized Enzymes andNanopore Direct RNA Sequencing

Nanopore direct RNA sequencing was performed using libraries preparedaccording to one of the five methods described in this example andillustrated in FIG. 1A-E. Total RNA from Listeria monocytogenes wasextracted using NEB Monarch Total RNA Miniprep Kit (NEB #T2010) andDNase I pack (NEB #T2019L) according the protocols of the manufacturer.The concentration of purified total RNA was measured using InvitrogenQubit™ RNA High-sensitivity Assay Kit (cat. Number: Q32852).

Details of RNA library preparation for each approach are discussedbelow. In all cases in this Example 4, sequencing preparation began with500 ng of each RNA as recommended by Oxford Nanopore Technologies. Forthe libraries prepared with soluble enzyme with bead purification,Nanopore's bead purification protocol was adopted. After beadpurification 20 μL of the resulting RNA library was mixed with 17.5 μLof nuclease-free water and 37.5 μL of RNA running buffer (provided byONT) to a final volume of 75 μL before loading into a flow cell fordirect RNA sequencing. For the libraries prepared with soluble enzymewithout bead purification, and immobilized enzymes, a portion of each 40μL RNA library was supplemented with nuclease-free water to 37.5 μL, andmixed with 37.5 μL RNA running buffer to a final volume of 75 μL.

Direct RNA sequencing was performed on a MinION® MkIb with R9.4 flowcells. MinKNOW® instrument software (ONT) recorded the nanopore currentas each strand of an adaptor-ligated RNA translocated through ananopore. Albacore 1.2.1 (ONT) was used to perform base-calling. Areport that displayed the major data sets was generated for eachsequencing. Major parameters, such as direct RNA reads and average readlength, were compared.

Example 4A. Soluble Poly(A) Polymerase without Bead Purification (FIG.1A)

For poly(A) tailing, mix 8 μL quick ligation buffer, 1.2 μL 5 M NaClsolution, 0.5 μL poly(A) polymerase (NEB M0276), and 500 ng totalListeria monocytogenes RNA, supplemented with nuclease-free water to 30μL in a 0.2 mL thin-walled PCR tube. Incubate the reaction at 37° C. for20 min. Next, for adaptor ligation, add 1.0 μL RT Adaptor (RTA), 6.0 μLRNA Adaptor (RMX) and 3.0 μL T4 DNA ligase (NEB M0202M) to the poly(A)tailed RNA sample to make a final volume of 40 μL. Incubate the reactionat 25° C. for 10 min RNA concentration was measured using the Qubitmethod after the enzymatic reaction (FIG. 1A). An aliquot of 40 μL RNAsample was used for further library prep as described above.

Example 4B. Sequential Reactions with Soluble Enzymes and BeadPurification (FIG. 1B)

Library preparation according to Example 4A was repeated with theaddition of a bead purification step after the enzymatic reactions.Specifically, 40 μL of resuspended NEBNext Sample Purification beads(E7104S) were combined with the adapter ligation reaction (40 μL) andmixed by pipetting and incubated on a Hula mixer (rotator mixer) at roomtemperature for 5 min. Samples were spun and pelleted on a magnet.Supernatant was pipetted off while pellets were retained on a magnet.Beads were combined with 150 μL of Wash Buffer (WSB) (150 μL) andresuspended by flicking the tubes. Tubes were returned to the magneticrack to allow beads to pellet and supernatant was removed by pipette.The wash step was repeated and the supernatant was removed. Each pelletwas resuspended in 21 μL Elution Buffer by gently flicking the tubeafter removal from the magnetic rack. Each tube was incubated at roomtemperature for 10 min to allow the elution of RNA. Beads were thenpelleted on a magnet until the eluate was clear and colorless. 21 μL ofeach eluate was removed and retained in a clean Eppendorf DNA LoBind®tube. 1 μL of RNA was used for concentration measurement using QubitAssay Kit. Final yield and recovery rate were determined. All 20 μL RNAsamples were used for further library prep as described above.

Example 4C. Coupled Reactions with Soluble Poly(A) Polymerase and BeadPurification (FIG. 1C)

For the coupled reactions approach using soluble enzymes, mix 8 μL quickligation buffer, 1.2 μL 5 M NaCl solution, 0.5 μL poly(A) polymerase(NEB M0276), 500 ng total RNA, 1.0 μL RT Adaptor (RTA), 6.0 μL RNAAdaptor (RMX) and 3.0 μL T4 DNA ligase (NEB M0202M) supplemented withnuclease-free water to 40 μL in a 0.2 mL thin-walled PCR tube. Incubatethe reaction at 37° C. for 20 min followed by 25° C. for 10 min to allowthe simultaneous poly(A) tailing and adaptor ligation. Samplepurification, RNA concentration determination, and further RNA libraryprep (using all 20 μL) were carried out as described in Example 4B.

Comparison of Nanopore direct RNA sequencing reads. Each library wasprepared using soluble enzyme with bead purification by sequential(Sol-seq) and coupled (Sol-cpl) reaction protocols for poly(A) tailingand adaptor ligation. Results are shown in FIG. 12.

Example 4D. Sequential Reactions with Immobilized Enzymes (FIG. 1D)

A model study was conducted by CE analysis of sequential treatment ofFAM-labeled RNA oligo (35mer) with immobilized poly(A) polymerase andimmobilized T4 DNA ligase. Poly(A) tailing was performed at 37° C. for20 min after mixing 6 μL nuclease-free water, 1 μL 10× poly(A)polymerase reaction buffer (NEB), 1 μL 10 mM ATP, 0.5 μL RNaseinhibitor, 1 μL 1 μM RNA 35-mer oligo (100 nM final concentration) and0.5 μL immobilized poly(A) polymerase (EXAMPLE 1C). Subsequently, afterremoval of immobilized PAP ligation was carried out at 25° C. for 10 minwith the addition of immobilized T4 DNA Ligase (provided by NEB, 60units/μL) and RTA-poly(dT)₁₅ or RTA-poly(dT)₁₀ (300 nM). Positiveresults were observed by CE analysis of the samples taken from thepoly(A) tailing reaction and adaptor ligation reactions (FIG. 13).

An RNA library was also prepared using immobilized enzymes using thesame workflow as described in Example 4B above except that the solubleenzymes (i.e. poly(A) polymerase and T4 DNA ligase) were replaced withtheir immobilized counterparts. Briefly, poly(A) tailing and ligationwere carried out sequentially by incubating RNA with 2.5 μL immobilizedPoly(A) polymerase at 37° C. for 20 min., removing the beads, incubatingthe supernatant with 3.0 μL immobilized T4 DNA ligase at 25° C. for 10min., and removing the beads with immobilized T4 DNA ligase Immobilizedenzymes, poly(A) polymerase in the first step and T4 DNA ligase in thesecond step, were separated from the reaction medium on a magnetic rackand the supernatant containing the products and other soluble componentswere transferred to a fresh tube for the subsequent reaction. No beadpurification was performed after the ligation of RTA and RMX adapters.The RNA concentration in the supernatant was determined using Qubitmethod. A portion of the 40 μL RNA library was supplemented withnuclease-free water to 37.5 μL, and mixed with 37.5 μL RNA runningbuffer to a final volume of 75 μL before loading into a flow cell fordirect RNA sequencing.

FIG. 14 shows that using immobilized enzymes yielded total reads andsequence length comparable to both soluble enzymes and beadpurification, indicating that immobilized enzymes can be used tosubstitute soluble enzymes in catalyzing poly(A) tailing and adaptorligation reactions. In addition, immobilized enzymes generated many moresequence reads than the soluble enzyme protocol incorporating no beadpurification. Thus, removal of the enzyme components from the RNAlibrary appears to be sufficient for generation of high sequence readsin nanopore sequencing presumably by avoiding clogging of nanopores byenzyme molecules. The soluble enzyme protocol without bead purificationyielded fewer reads, suggesting that proteins or other components in thereaction mixture may cause nanopore fouling. Soluble enzyme protocolwith bead purification also displayed fewer reads probably due toimpurities as the result of bead purification.

Example 4E. Coupled Reactions with Immobilized Enzymes (FIG. 1E)

The sequential poly(A) tailing and ligation steps (shown in Example 4D)were combined into a single, coupled reaction as shown in FIG. 1E.Poly(A) tailing and ligation were carried out by using 2.5 μLimmobilized Poly(A) polymerase and 3.0 μL immobilized T4 DNA ligasetogether at 37° C. for 20 min followed by 25° C. incubation for 10 min.The immobilized enzyme beads were separated from the reaction medium onmagnetic rack and the supernatant containing the products and othersoluble components were transferred to a fresh tube. A library was alsoprepared using the sequential reaction protocol with immobilized enzymesdescribed in EXAMPLE 4D.

The RNA concentration in the resulting libraries was determined usingQubit method. The same amount of RNA from each library was used toprepare the sequencing mixtures supplemented with nuclease-free water toa volume of 37.5 μL and another 37.5 μL of RNA running buffer (RRB) wereused to prepare 75 μL sample for RNA sequencing according to Example 2D.Direct RNA sequencing for both sequential (Example 2C) and coupledreaction (this example) were performed on a MinION® MkIb with R9.4 flowcells as introduced before.

Results shown in FIG. 15 contrast the number of sequencing read from thecoupled reaction protocol to that of the sequential reaction protocolusing immobilized enzymes. The library prepared using a sequentialreaction strategy (Example 4D) with an RNA sequencing input of 105 ng ofRNA yielded 459 K reads, which is comparable to the results presented inExample 4C with final yield of 488.5 K reads from 164.4 ng of RNA input.However, the library prepared in this Example using a coupled reactionprotocol with immobilized enzymes with similar amount of RNA inputproduced almost a 3-fold increase in RNA sequencing reads compared to asequential reaction protocol using immobilized enzymes.

Example 4F. Coupled Reactions with Co-Immobilized Enzymes

O⁶-benzylguainine (BG) functionalized magnetic beads coated with PEG₇₅₀(100 μL of a 25% (v/v) slurry) were used for enzyme co-immobilization.Poly(A) polymerase-SNAP fusion protein and T4 DNA ligase-SNAP fusionprotein (12.5 μg of each) were dissolved in 125 μL buffer (1×PBS with300 mM NaCl), combined with the washed BG beads, and incubated at 4° C.overnight to immobilize the fusion protein on the beads, according tothe procedure described in EXAMPLE 1C. The co-immobilized beads werewashed with the same buffer 8 times to remove any unbound enzymemolecules. Diluent A buffer without BSA (NEB) with 100 mM NaCl was usedto resuspend the beads with immobilized fusion protein for storage at−80° C.

Poly(A) tailing and adaptor ligation activities were measured for thebead sample co-immobilized with poly(A) polymerase and T4 DNA ligase. 5μL of the co-immobilized enzyme bead mixture were used to replace 2.5 μLimmobilized poly(A) polymerase and 3 μL immobilized T4 DNA ligase ineach activity assay. The co-immobilized enzymes displayed both poly(A)polymerase activity (FIG. 16A) and T4 DNA ligase activity (FIG. 16B).

Example 5: Automated Library Construction and Sequencing

While next-generation sequencing (NGS) has greatly advancing biologicalresearch and clinical diagnostics, the process would benefit fromautomation from library construction to sequencing libraries and dataanalysis. The preceding examples demonstrate that application ofimmobilized enzymes in multi-reaction library construction workflowsavoids bead based nucleic acid purification which may cause sample lossand bias in fragment distribution. Combining the single-reactionpreparation of Example 4 with NGS (e.g., using robotics and/ormicrofluidics) advances automation in sequencing. Specifically,otherwise cumbersome steps of adding adapters to nucleic acid librariesto be sequenced may be in a single reaction vessel and fed directly intosequencing platforms. The concomitant reduction in handling will reduceerror rates and variations in high-throughput research and clinicalapplication of Nanopore and other NGS technologies (FIG. 17).

As shown, magnetic beads bearing enzymes are positioned in properenclosed chamber and tunnel to process an input or intermediate library.There is no extra purification step required for separation of theenzymes and the resulting products, between or after enzymatic reactionsteps. The input library can be produced by a method, for example, RNAextraction, that incorporates a properly designed automated workflow. Anoutput library can be properly formulated for direct sequencing on ananopore sequencing device, i.e. flow cell, such as currently availableR9.4.1. or R10. Ultimately, this workflow is linked to locally based orcloud-based computer software to provide a fully automated sequencingsolution.

Example 6: Direct RNA Sequencing with Low Input RNA is Possible whenImmobilized Enzymes are Used in Library Prep

All sequencing reads using the libraries described in Example 4 wereperformed with 500 ng of RNA as suggested by Oxford NanoporeTechnologies. This example demonstrates construction and successfulsequencing of duplicate libraries from a lower initial input (100 ng) ofListeria monocytogenes RNA using either a sequential or coupled reactionprotocol with immobilized poly(A) polymerase and T4 DNA Ligase. Forsequential reaction protocol, 3 μL quick ligation buffer, 0.45 μL 5 MNaCl solution, 1.5 μL immobilized poly(A) polymerase, and 100 ng totalRNA, supplemented with nuclease-free water to 10 μL were mixed in a 0.2mL thin-walled PCR tube and incubated at 37° C. for 20 min for poly(A)tailing. After immobilized poly(A) polymerase beads were removed byplacing the tube on the magnetic rack, 0.5 μL RT Adaptor (RTA), 3.0 μLRNA Adaptor (RMX) and 1.5 μL immobilized T4 DNA ligase were added to thepoly(A) tailed RNA sample to yield a final volume of 15 μL. This mixturewas incubated at 25° C. for 10 min for adaptor ligation. The immobilizedligase was removed using the magnet. For the coupled reaction protocol,the same amounts of enzymes and buffer were utilized as disclosed above(except that all the components were combined in a single tube). Themixtures were incubated at 37° C. for 20 min and 25° C. for 10 min,consecutively, and both immobilized enzymes were removed in a singlestep on the magnetic rack. The RNA yields of the prepared libraries weredetermined by high sensitivity RNA Qubit assay.

With the initial RNA input of 100 ng, the sequential and coupledreaction methods resulted in recovery of an average of 38 ng and 83 ng,respectively, from duplicate libraries. Thus, the recovery rate for RNAlibrary prep using the coupled reaction protocol is 83% of the initialinput, much higher than that of the sequential reaction protocol (FIG.18A). The results also suggest that a coupled reaction process generatesmore reads compared to the sequential reaction. In addition, asequential reaction generates 568 K reads on average, higher than thatobtained from the protocol using soluble enzymes with bead purification.The results demonstrate that low input RNA library construction can beachieved by using both sequential and coupled reaction protocols withimmobilized enzymes (FIG. 18A).

Similar results were obtained with library construction from a lowinitial input mammalian human brain RNA (100 ng). FIG. 18B shows directRNA sequencing of low input of poly(A) tailed human RNA (100 ngPolyA+RNA) prepared by ligation to RTA and RMX adaptors with immobilizedT4 DNA Ligase (ImL) Furthermore, total mammalian RNA library (100 nginput), prepared with immobilized poly(A) polymerase and immobilized T4DNA ligase (ImP and ImL) using the coupled reaction protocol describedabove in this example, was successfully used for direct RNA sequencing.

Example 7: Metrics of the ONT Direct RNA-Seq Datasets from VariousLibrary Preparation Protocols

Duplicate libraries using each of the five RNA library preparationprotocols were made with 500 ng input RNA extracted from Listeriamonocytogenes (ATCC 1115) culture. The final volume for the enzymaticreactions was 40 μl prior to bead purification; for soluble enzymeprotocols, Sol-seq and Sol-cpl, each RNA library was further purifiedwith RNA binding beads and eluted in 20 μl volume. For immobilizedenzyme protocols enzyme removal was performed without purification usingRNA binding beads prior to use of a fraction of the library sample forNanopore direct RNA sequencing. Results are shown in TABLE 1.

TABLE 1 500 ng input libraries Sol-seq Sol-cpl Im-seq Replicate R1 R2Avg Std R1 R2 Avg Std R1 R2 FAM9 FAM9 FAM9 FAN2 FAN2 FAN2 6082 4718 47893186 7746 7699 Recovery 29% 39% 34% 34% 34% 34% 31% 47% rate Loading 176197 186 196 222 209 88 116 (ng) Loading 20 20 20 20 20 20 (μL) Reads 134149 141 8 642 757 699 58 903 798 generated (K) Bases 136 168 152 16 681816 748 68 836 737 generated (Mb) Estimated 157 200 178 21 829 962 89566 1030 896 generated (Mb) Bases/ 0.86 0.84 0.85 0.82 0.85 0.84 0.810.82 Estimated Run 18 22 20 45 53 49 40 40 Length (hr) 500 ng inputlibraries Im-seq Im-cpl Sol w/o BP Replicate Avg Std R1 R2 Avg Std R1 R2Avg Std FAM9 FAN0 FAL6 FAL7 4697 3228 8474 0280 Recovery 39% 100% 117%108% rate Loading 102 176 197 186 (ng) Loading 11 15.6 (μL) Reads 850 521580 1070 1325 255 430 226 328 102 generated (K) Bases 786 50 1610 11201365 245 427 146 286 140 generated (Mb) Estimated 963 67 2000 1390 1695305 526 192 359 167 generated (Mb) Bases/ 0.82 0.81 0.81 0.81 0.81 0.760.80 Estimated Run 40 72 72 72 43 21 32 Length (hr)

Example 8: Comparison of the Major Metrics of the ONT Direct RNA-SeqDatasets from Various Library Preparation Methods

The average of the major metrics from duplicate libraries prepared usingeach of the five RNA library preparation protocols were analyzed. Eachlibrary was made with 500 ng input RNA extracted from Listeriamonocytogenes (ATCC 1115) culture. The final volume for the enzymaticreactions was 40 μl prior to bead purification; for soluble enzymeprotocols, Sol-eq and Sol-cpl, each RNA library was further purifiedwith RNA binding beads and eluted in 20 μl volume. For immobilizedenzyme protocols enzyme removal was performed without purification usingRNA binding beads prior to use of a fraction of the library sample forNanopore direct RNA sequencing.

Averages of two replicate runs are shown in TABLE 2.

TABLE 2 500 ng input libraries Sol-seq Sol-cpl Im-seq Im-cpl Recoveryrate 0.34 0.34 0.39 1.08 Loading (ng) 186.4 208.8 102.0 186.4 Loading(μL) 20 20 20 13.3 Reads generated (K) 141.42 699.33 850.42 1325 Basesgenerated (Mb) 151.58 748.15 786.34 1365 Estimated generated 178.2 895.4963.11 1695 (Mb) Bases/Estimated 0.85 0.84 0.82 0.81 Run Length (hr)20.2 48.8 40.3 72.0 Mean read length 1145.3 1156.4 1065.9 1107.9 (nt)Median read length 1157 1028 950 951 (nt) Read length N50 1493 1520 14641511 Mean read quality 10.2 10.1 10.2 10.2 Median read quality 10.4 10.210.4 10.3 Mapping 99.6% 99.2% 99.3% 99.1% Mapped reads 140.84 693.52844.55 1313.08 Expected Reads 141.4 699.3 1615.8 3902.4 (K)/LibraryExpected bases 151.6 748.2 1494.0 4020.2 (Mb)/Library Ratio of Expected1 4.9 11.4 27.6 Reads (K)/Library

Example 9: Comparison of Nanopore Direct RNA Sequencing Reads

Duplicate libraries were prepared using the five protocols illustratedin FIG. 1A-E. Each library was made with 500 ng input RNA extracted fromListeria monocytogenes (ATCC 1115) culture. For Sol-seq and Sol-cpl,each RNA library was further purified with RNA binding beads prior toNanopore sequencing. Both immobilized enzyme protocols did not utilize apurification step with RNA-binding beads after enzymatic treatment, andenzyme removal was performed with magnetic rack prior to sequencing.Results are shown in FIG. 19.

Example 10: Reduced Inactivation of Nanopores Using Libraries Preparedwith Immobilized Enzymes

Data presented in Examples 7-9 demonstrates that bead purificationfollowing library preparation with soluble enzymes is associated with aconsiderable loss of library RNA. Example 13 shows further that omittinga bead purification step (to avoid this loss of RNA) may not be afavorable solution in that the resulting libraries produce substantiallyfewer sequence reads from the same amount of input RNA compared to theimmobilized enzyme protocols. A possible reason for fewer sequence readsfrom the libraries produced by the soluble enzyme protocol without beadpurification is that residual polymerase and/or ligase may occludenanopores. On the other hand, bead purification may affect libraryquality due to loss of RNA (or certain RNA types) and may also produceimpurity derived from the wash solutions. In this example, the activityof nanopores was monitored over the course of a sequencing run fromMinKNOW® report. Results shown in FIG. 20 demonstrate that morenanopores remain active (upper trace) when the libraries were preparedwith immobilized enzymes compared to those prepared with solubleenzymes. For example, after two hours of sequencing, about 90% of thepores processing immobilized enzyme libraries remained active while onlyabout 65% of the pores processing soluble enzyme libraries remainedactive. At 8 hours, about half of the pores processing immobilizedenzyme libraries remained active while only about 10% of the poresprocessing soluble enzyme libraries remained active. These resultsdemonstrate that the use of immobilized enzymes in library constructioncan increase nanopore sequencing output, possibly by reducing nanoporefouling.

The number of reads per pore was also evaluated for the coupled reactionmethod. Normalized reads shown in FIG. 21 were generated from dividingthe reads from sequencing a Listeria RNA library by the number of pores.

Three Listeria RNA libraries were prepared using the coupled reactionprotocol using immobilized enzymes (orange dots). Two low input RNAlibraries were prepared in 15 uL following the coupled reaction protocolas described in Example 5, resulting in direct RNA sequencing of 83 ngand 136.5 ng RNA per flow cell, respectively. The third library wasprepared as described in Example 4E with 500 ng input RNA in 40 uL andonly part of the resulting library (109 ng) was loaded for sequencing.

The number of reads per pore was also examined for a set of fourlibraries prepared using the sequential reaction protocol usingimmobilized enzymes (blue dots). Two low input RNA libraries wereprepared in 15 uL as described in Example 5, resulting in sequencing 38ng and 39 ng RNA per flow cell, respectively. Two 500 ng input RNAlibraries were made in 40 uL as described in Example 4D and a portion ofeach resulting library, 105 ng and 164.4 ng, respectively, was used forloading on a flow cell and direct RNA sequencing.

Results indicate that the coupled reaction protocol can generate asignificantly higher reads per nanopore compared to the sequentialreaction protocol using the same set of immobilized enzymes andconditions (i.e. buffer, total reaction time and volume).

Example 11: DNA Library Construction Workflow for Nanopore Sequencing ofUltra-Long Templates without Bead Purification

This example describes a new strategy for preparation of DNA librariesfor nanopore DNA sequencing. The current ONT protocol, as depicted inFIG. 26 and Example 13, utilizes a set of four DNA-modifying enzymes toperform end-polishing, dA-tailing and adaptor ligation, in conjunctionwith bead purification to produce a library for long-read sequencing.Addition of a single 3′A in dA-tailing demands use of PEG in thesubsequent adaptor ligation because T/A pairing is inefficient in theabsence of PEG or other enhancers. However, use of PEG in conjunctionwith use of AMPure® beads may not be ideal since PEG can cause DNAcompaction onto beads. In addition, application of bead purification canresult in shearing of long DNA templates thereby adversely affecting theability of ultra-long sequence reads by nanopore sequencing.

A new method is proposed here and illustrated in FIG. 22. As shown, theproposed method does not use bead purification and/or may include orexclude use PEG during DNA library preparation. This workflow iscomprised of three major enzymatic steps. First, Terminaldeoxynucleotidyl transferase (TdT) is employed to catalyze poly(dA)tailing at 3′ end of DNA fragments possibly pre-treated withend-polishing enzyme(s). The oligo(dA) overhang can then efficientlyligate with an adaptor with a 3′ Poly(dT) overhang and motor protein, inthe presence or absence of PEG in the reaction medium. Next, gap-fillingand nick sealing can be accomplished with DNA polymerase and DNA Ligase.Enzymes may be removed, inactivated or present in the final sequencinglibrary. Breakage of DNA molecules may be reduced and/or recovery oflong DNA templates may be improved by avoiding use of bead purificationand/or PEG. As practitioners having the benefit of this disclosure willappreciate, TdT can add other types of oligos, such as poly(dT) orpoly(dG) to be suitable for other adaptor ligation strategies in theabsence of PEG or DNA-compacting factor. Thus, different enzymes andtailing approaches can be designed to prepare DNA-adaptor moleculesanchored with motor protein and other features required for nanoporesequencing.

Example 12: DNA Library Preparation

This example demonstrates poly(dA) tailing of a synthetic DNA substrateand subsequent ligation of the products possessing various lengths of 3′poly(dA) sequences to an adaptor having a 3′ poly(dT) overhang asillustrated in FIG. 23.

Example 6A. Poly(dA)-Tailing Mediated by Terminal DeoxynucleotidylTransferase (TdT)

This example demonstrates poly(dA) tailing of a synthetic DNA substrateby Terminal deoxynucleotidyl Transferase (TdT). A double-stranded DNAsubstrate was formed by annealing two oligonucleotides, with onepossessing a 5′ fluorophore probe, FAM and 3′ protruding overhang foraddition of Poly(dA) tails. 5′FAM-labeled double-stranded DNA wastreated with TdT in the presence of various concentrations of dATP tocreate different substrate to dATP ratios (e.g. 1:100 and 1:200). CEanalysis was performed to assess the incorporation of dAMP at the 3′termini of 5′FAM-labeled DNA strand and estimation of the lengths (orrange) of poly(dA) tails.

3′ poly(dA) tailing was carried out in a 30 μl reaction volume in thepresence of 0.1 μM of the DNA substrate, 0.5 μl (20 units) of TdT (NEB,M0315S, 40,000 units/ml,), 1×TdT Reaction Buffer (NEB), 0.25 mM CoCl₂and 10 or 20 μM of dATP. The reactions were performed at 37° C. for 30min, followed by treatment at 70° C. for 10 min in a T-100 Thermocycler(Bio-Rad Laboratories, Hercules, Calif.). The reactions were terminatedby diluting in 1:1 ratio in 50 mM EDTA and 0.1% Tween-20, and analyzedby CE technique and Peak Scanner software. Results shown in FIG. 24Ademonstrate that poly(dA) tailing can be performed in 1×TdT buffersupplemented with CoCl₂. Efficient conversion of the DNA substrate topoly(dA) tailed products of various lengths was observed after treatmentwith TdT and the length of the poly(dA) can be modulated by the controlof substrate-to-dATP ratio.

Example 12B. Sequential Poly(dA) Tailing and Adaptor Ligation

The FAM-labeled double-stranded DNA substrate was assayed for sequentialpoly(dA) tailing with soluble TdT as described in EXAMPLE 12A andadaptor ligation with soluble T4 DNA Ligase.

A modified RTA adaptor, RTA-Poly(dT) was made by annealing twooligonucleotides, derived from the sequences of RTA (provided by ONT),with one oligonucleotide containing 5′ phospho group and 3′ ROX probe,and the second one being modified to possess 3′ poly(dT).3′ poly(dA)tailing was carried out in a 30 μl reaction volume in the presence of0.1 μM of the DNA substrate, 1 unit of Terminal DeoxynucleotideTransferase (NEB, M0315S, 40,000 units/ml,), 1×TdT Reaction Buffer(NEB), 0.25 mM CoCl₂ and 10, 20 or 50 μM of dATP. The reactions wereperformed at 37° C. for 30 min, followed by treatment at 70° C. for 10min in a T-100 Thermocycler (Bio-Rad Laboratories, Hercules, Calif.).Next, adaptor ligation was performed at 25° C. for 30 min after additionof 100 nM RTA-poly(dT), 1 mM ATP and 1 μl of T4 DNA Ligase (NEB, M0202S,400,000 units/μl) to the TdT-treated samples. The reactions wereterminated by diluting in 50 mM EDTA and 0.1% Tween-20, and analyzed byCE technique and Peak Scanner software. Efficient conversion of the DNAsubstrate to poly(dA) tailed products of various lengths was observedafter treatment with TdT. Joining of poly(dA) tailed products andmodified RTA was also detected because of the shift of the FAM labeledproducts and the co-localization of FAM and ROX signals after ligationreaction, in comparison with the TdT-treated sample.

FIG. 24B shows a peak formed by a range of FAM-labeled products (inblue), representing various 3′ poly(dA) lengths. Subsequently, thereaction medium containing the poly(dA)-tailed DNA products, wasincubated with T4 DNA ligase and RTA-poly(dT) adaptor possessing 3′poly(dT) and 5′ ROX. FIG. 24C shows co-localization of the fluorescencesignals of FAM (blue) and ROX (red) indicates ligation of the5′FAM-labeled DNA species to the 3′ ROX-labeled strand of the adaptor.Successful ligation also resulted in a shift of the FAM-labeled species(major peak in TdT sample) to higher molecular products (major Peak inTdT/T4 DNA Ligase sample).

Results shown FIG. 24B and FIG. 24C demonstrate that both poly(dA) andligation reactions can be performed in 1×TdT buffer supplemented withCoCl₂.

Example 12C. Ligation of Poly(dA) Tailed DNA with Adaptor with Solubleand Immobilized Ligase

As shown in FIG. 25, a FAM-labeled double-stranded DNA substrate wasfirst tailed using soluble TdT as described in EXAMPLE 6A and thenligated to an adapter with either soluble or immobilized T4 DNA Ligase.3′ poly(dA) tailing was carried out in a 30 μl reaction volume in thepresence of 0.1 μM of the DNA substrate, 1 unit of TerminalDeoxynucleotide Transferase (NEB, M0315S, 40,000 units/ml,), 1×TdTReaction Buffer (NEB), 0.25 mM CoCl₂ and 10, 20 or 50 μM of dATP. Thereactions were performed at 37° C. for 30 min, followed by treatment at70° C. for 10 min in a T-100 Thermocycler (Bio-Rad Laboratories,Hercules, Calif.). Next, adaptor ligation was performed at 25° C. for 30min after addition of 100 nM RTA-poly(dT), 1 mM ATP and 1 μl of T4 DNALigase (NEB, M0202S, 400,000 units/μl) or immobilized T4 DNA Ligase(NEB, Production Lot 1, 60 units/μl) to the TdT-treated samples. Thereactions were terminated by diluting in 50 mM EDTA and 0.1% Tween-20,and analyzed by CE technique and Peak Scanner software. Efficientconversion of the DNA substrate to poly(dA) tailed products of variouslengths was observed after treatment with TdT. Poly(dA) tailed productsand modified RTA were detected with either soluble or immobilized T4 DNAligase because of the shift of the FAM labeled products and theco-localization of FAM and ROX signals after ligation reaction, incomparison with the TdT-treated sample. These results show that bothpoly(dA) and ligation reactions can be performed in 1×TdT buffersupplemented with CoCl₂.

Example 13: DNA Library Construction Using Immobilized DNA ModifyingEnzymes

Many existing methods rely on steps (e.g., AMPure® bead purification)that shear long DNA molecules and are detrimental to long-readsequencing. In addition to use for RNA library preparation forsequencing, immobilized enzymes can be used to construct DNA libraries.FIG. 26 shows a schematic of DNA library construction using a set offour immobilized DNA modifying enzymes (IM-T4 DNA polymerase IM-T4 PNK,IM-Taq DNA Pol, IM-T4 DNA Ligase). Soluble forms of these enzymes arecurrently used for Nanopore DNA library construction. The followingexample sets forth the use of relevant immobilized enzymes to generate aDNA library by using an oligo DNA model system with a CE technique toconduct step-by-step analyses.

Example 14: DNA Library Construction Using Immobilized DNA ModifyingEnzymes

A DNA library construction protocol for nanopore sequencing may includefragmentation, end repair (blunting and 5′ phosphorylation), 3′A-tailing and adaptor ligation. Once the sample DNA has been sheared,the fragment ends are repaired by blunting and 5′ phosphorylation with amixture of enzymes, such as T4 polynucleotide kinase (PNK) and T4 DNApolymerase (T4 DNA pol). This end repair step is followed by 3′A-tailing at 37° C. using a mesophilic polymerase such as KlenowFragment 3′-5′ exonuclease minus¹¹, or at elevated temperatures using athermophilic polymerase such as Taq DNA polymerase (Taq DNA pol) (Head,S. R. et al. Library construction for next-generation sequencing:overviews and challenges. BioTechniques 56, 61-64, 66, 68, passim(2014); Star, B. et al. Palindromic Sequence Artifacts Generated duringNext Generation Sequencing Library Preparation from Historic and AncientDNA. PLOS ONE 9, e89676 (2014)). 3′ A-tailed DNA fragments are ligatedto an adaptor using a T/A ligation method and purified using AMPure®beads prior to nanopore sequencing. Bead-based purification step(s) mayresult in shearing large DNA which is detrimental to long readsequencing. In addition, T/A ligation efficiency is highly dependent onthe presence of crowding agent, such as PEG, however, use of a crowdingagent, namely PEG, appears to cause large DNA molecules to compact(Warren M. Mardoum, Stephanie M. Gorczyca, Kathryn E. Regan, Tsai-ChinWu, and Rae M. Robertson-Anderson. Crowding Induces Entropically-DrivenChanges to DNA Dynamics That Depend on Crowder Structure and IonicConditions. Front Phys. 2018; 6: 53; Heikki Ojal, Gabija Ziedait, AndersE. Wallin, Dennis H. Bamford, Edward Hæggström. Optical tweezers revealforce plateau and internal friction in PEG-induced DNA condensation.European Biophysics Journal, March 2014, Volume 43, Issue 2-3, pp71-79). Consequently, the PEG-induced DNA compaction may reduce DNAelution from AMPure® beads, resulting in low library yield of large DNA.

An enzyme immobilization strategy was previously utilized to perform DNAlibrary construction for the sequencing on the Illumina platform (Zhang,Aihua, et al. Solid-phase enzyme catalysis of DNA end repair and 3′A-tailing reduces GC-bias in next-generation sequencing of human genomicDNA. Scientific reports 8.1 (2018): 1-11.). The relevant DNA-modifyingenzymes were produced as SNAP-tagged fusion proteins and immobilized bycovalent conjugation onto magnetic beads functionalized with benzylguanine ligand (the substrate of SNAP-tag). These immobilized enzymeswere successfully applied to Illumina DNA library construction in placetheir soluble counterparts. One of the major of the major advantages isthat the enzymes can be removed without heat treatment or AMPure® beadpurification.

This example demonstrates that the same set of enzymes can be used forthe current workflow of Nanopore DNA library construction. In thisexample, each enzymatic reaction step was monitored by fluorescencecapillary gel electrophoresis (CE) using a synthetic double stranded DNAend-labeled with a fluorescent probe, FAM. DNA was end-repaired for 30min at 20° C. using immobilized T4 DNA pol and T4 polynucleotide kinasein a 20 reaction in the presence of 1×NEBNext End Repair Buffer II.These end-repair enzymes were pelleted on a magnetic rack and thesupernatant was transferred to a new tube for 3′ A-tailing withimmobilized Taq DNA pol at 37° C. for 30 min. The resulting product wasligated to an adaptor with an end possessing 5′ phospho group and 3′T.The reactions were terminated by diluting in 50 mM EDTA and 0.1%Tween-20. The reactions were performed in a T-100 Thermocycler (Bio-RadLaboratories, Hercules, Calif.) and analyzed by CE technique and PeakScanner software. A partial ligation of the DNA substrate to the adaptoris shown in FIG. 27, indicating that T/A ligation can be performed in1×NEBNext End Repair Buffer II without supplement with PEG.

What is claimed is:
 1. A method of preparing a library for sequencing,comprising: (a) in a coupled reaction, (i) contacting a population ofnucleic acid fragments with a tailing enzyme to produce tailedfragments, and (ii) ligating to the tailed fragments a sequencingadapter with a ligase to produce adapter-tagged fragments; and (b)separating adapter-tagged fragments from the tailing enzyme and theligase to produce separated adapter-tagged fragments and, optionally,separated tailing enzyme and/or separated ligase.
 2. A method accordingto claim 1, wherein the tailing enzyme and the ligase are immobilizedenzymes.
 3. A method according to claim 1, wherein the tailing enzyme isimmobilized on a magnetic bead.
 4. A method according to claim 3,wherein the separating the adapter tagged fragments further comprisessubjecting the coupled reaction to a magnetic field.
 5. A methodaccording to claim 1, wherein the ligase is immobilized on a magneticbead.
 6. A method according to claim 5, wherein the separating theadapter tagged fragments further comprises subjecting the coupledreaction to a magnetic field.
 7. A method according to claim 1, whereinthe tailing enzyme and the ligase are immobilized on separate supports.8. A method according to claim 1, wherein the coupled reaction stepsoccur in a single tube, well, capillary, flow cell or surface.
 9. Amethod according to claim 1, wherein the tailing enzyme and the ligaseare soluble enzymes.
 10. A method according to claim 1, wherein thepopulation of nucleic acid fragments comprise ribonucleic acidfragments.
 11. A method according to claim 1, wherein the population ofnucleic acid fragments comprise deoxyribonucleic acid fragments.
 12. Amethod according to claim 1, wherein the population of nucleic acidfragments has less than 100 ng of nucleic acids.
 13. A method accordingto claim 1, wherein the population of nucleic acid fragments has lessthan 10 ng of nucleic acids.
 14. A method according to claim 1, furthercomprising: (c) in a second coupled reaction, (i) contacting a secondpopulation of nucleic acid fragments with the separated tailing enzymeto produce additional tailed fragments, and (ii) ligating to theadditional tailed fragments a second sequencing adapter with theseparated ligase to produce additional adapter-tagged fragments, and (d)separating the additional adapter-tagged fragments from the separatedtailing enzyme and the separated ligase to produce separated additionaladapter-tagged fragments, separated tailing enzyme, and separatedligase.
 15. A method according to claim 14, further comprising: (e)translocating the separated adapter-tagged fragments through one or moretransmembrane pores; (f) detecting electrical changes as the one or moreseparated adapter-tagged fragments are translocated through the one ormore transmembrane pores in an insulating membrane to produce anelectrical signal; and (g) analyzing the electrical signal to generate asequence read.
 16. A method according to claim 15, wherein the one ormore transmembrane pores retain about 90% of their initial activityafter two hours.
 17. A method according to claim 15, wherein the one ormore transmembrane pores retain about 50% of their initial activityafter 8 hours.
 18. A method according to claim 15, wherein the one ormore transmembrane pores produce at least 900 sequence reads pertransmembrane pore.
 19. A method according to claim 1, wherein thesequencing adapter is a single stranded adapter comprising: a leadersequence; and a first sequence and a second sequence, wherein the firstand second sequences are complementary to each other and define ahairpin, wherein the leader sequence is configured to thread into theone or more transmembrane pores.